diff --git a/prepare/r-annotationdbi/PKGBUILD b/prepare/r-annotationdbi/PKGBUILD deleted file mode 100644 index 6f88bb9444..0000000000 --- a/prepare/r-annotationdbi/PKGBUILD +++ /dev/null @@ -1,48 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=AnnotationDbi -_pkgver=1.56.2 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Manipulation of SQLite-based annotations in Bioconductor' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biobase - r-biocgenerics - r-dbi - r-iranges - r-keggrest - r-rsqlite - r-s4vectors -) -optdepends=( - r-annotationforge - r-biocstyle - r-ensdb.hsapiens.v75 - r-go.db - r-graph - r-hgu95av2.db - r-knitr - r-org.at.tair.db - r-org.hs.eg.db - r-org.sc.sgd.db - r-reactome.db - r-runit - r-txdb.hsapiens.ucsc.hg19.knowngene -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationdbi/lilac.py b/prepare/r-annotationdbi/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-annotationdbi/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-annotationdbi/lilac.yaml b/prepare/r-annotationdbi/lilac.yaml deleted file mode 100644 index 1f98b31082..0000000000 --- a/prepare/r-annotationdbi/lilac.yaml +++ /dev/null @@ -1,16 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biobase -- r-biocgenerics -- r-dbi -- r-iranges -- r-keggrest -- r-rsqlite -- r-s4vectors -update_on: -- regex: AnnotationDbi_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/AnnotationDbi diff --git a/prepare/r-askpass/PKGBUILD b/prepare/r-askpass/PKGBUILD deleted file mode 100644 index c8ac365705..0000000000 --- a/prepare/r-askpass/PKGBUILD +++ /dev/null @@ -1,31 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=askpass -_pkgver=1.1 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Safe Password Entry for R, Git, and SSH' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('MIT') -depends=( - r - r-sys -) -optdepends=( - r-testthat -) -source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-askpass/lilac.py b/prepare/r-askpass/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-askpass/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-askpass/lilac.yaml b/prepare/r-askpass/lilac.yaml deleted file mode 100644 index 382482abbc..0000000000 --- a/prepare/r-askpass/lilac.yaml +++ /dev/null @@ -1,10 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-sys -update_on: -- regex: askpass_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=askpass diff --git a/prepare/r-assertthat/PKGBUILD b/prepare/r-assertthat/PKGBUILD deleted file mode 100644 index 78e512dddc..0000000000 --- a/prepare/r-assertthat/PKGBUILD +++ /dev/null @@ -1,30 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=assertthat -_pkgver=0.2.1 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Easy Pre and Post Assertions' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') -depends=( - r -) -optdepends=( - r-covr - r-testthat -) -source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertthat/lilac.py b/prepare/r-assertthat/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-assertthat/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-assertthat/lilac.yaml b/prepare/r-assertthat/lilac.yaml deleted file mode 100644 index bbc7a4e6b1..0000000000 --- a/prepare/r-assertthat/lilac.yaml +++ /dev/null @@ -1,8 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -update_on: -- regex: assertthat_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=assertthat diff --git a/prepare/r-biobase/PKGBUILD b/prepare/r-biobase/PKGBUILD deleted file mode 100644 index 2302e084f6..0000000000 --- a/prepare/r-biobase/PKGBUILD +++ /dev/null @@ -1,34 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=Biobase -_pkgver=2.54.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Biobase: Base functions for Bioconductor' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics -) -optdepends=( - r-all - r-golubesets - r-runit - r-tkwidgets - r-tools -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biobase/lilac.py b/prepare/r-biobase/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biobase/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biobase/lilac.yaml b/prepare/r-biobase/lilac.yaml deleted file mode 100644 index 3295171afd..0000000000 --- a/prepare/r-biobase/lilac.yaml +++ /dev/null @@ -1,10 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -update_on: -- regex: Biobase_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/Biobase diff --git a/prepare/r-biocfilecache/PKGBUILD b/prepare/r-biocfilecache/PKGBUILD deleted file mode 100644 index c46e08e6ab..0000000000 --- a/prepare/r-biocfilecache/PKGBUILD +++ /dev/null @@ -1,41 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=BiocFileCache -_pkgver=2.2.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Manage Files Across Sessions' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-curl - r-dbi - r-dbplyr - r-dplyr - r-filelock - r-httr - r-rappdirs - r-rsqlite -) -optdepends=( - r-biocstyle - r-knitr - r-rmarkdown - r-rtracklayer - r-testthat -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocfilecache/lilac.py b/prepare/r-biocfilecache/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biocfilecache/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biocfilecache/lilac.yaml b/prepare/r-biocfilecache/lilac.yaml deleted file mode 100644 index 96eb932715..0000000000 --- a/prepare/r-biocfilecache/lilac.yaml +++ /dev/null @@ -1,17 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-curl -- r-dbi -- r-dbplyr -- r-dplyr -- r-filelock -- r-httr -- r-rappdirs -- r-rsqlite -update_on: -- regex: BiocFileCache_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BiocFileCache diff --git a/prepare/r-biocgenerics/PKGBUILD b/prepare/r-biocgenerics/PKGBUILD deleted file mode 100644 index c92d5d2448..0000000000 --- a/prepare/r-biocgenerics/PKGBUILD +++ /dev/null @@ -1,43 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=BiocGenerics -_pkgver=0.40.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='S4 generic functions used in Bioconductor' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r -) -optdepends=( - r-affy - r-affyplm - r-annotate - r-annotationdbi - r-biobase - r-biostrings - r-delayedarray - r-deseq2 - r-flowclust - r-genomicranges - r-iranges - r-msnbase - r-rsamtools - r-runit - r-s4vectors -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocgenerics/lilac.py b/prepare/r-biocgenerics/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biocgenerics/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biocgenerics/lilac.yaml b/prepare/r-biocgenerics/lilac.yaml deleted file mode 100644 index b74b3a2e27..0000000000 --- a/prepare/r-biocgenerics/lilac.yaml +++ /dev/null @@ -1,8 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -update_on: -- regex: BiocGenerics_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BiocGenerics diff --git a/prepare/r-biocio/PKGBUILD b/prepare/r-biocio/PKGBUILD deleted file mode 100644 index 6b6f5ca40b..0000000000 --- a/prepare/r-biocio/PKGBUILD +++ /dev/null @@ -1,34 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=BiocIO -_pkgver=1.4.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Standard Input and Output for Bioconductor Packages' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-s4vectors -) -optdepends=( - r-biocstyle - r-knitr - r-rmarkdown - r-testthat -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocio/lilac.py b/prepare/r-biocio/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biocio/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biocio/lilac.yaml b/prepare/r-biocio/lilac.yaml deleted file mode 100644 index fd24ae7649..0000000000 --- a/prepare/r-biocio/lilac.yaml +++ /dev/null @@ -1,11 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-s4vectors -update_on: -- regex: BiocIO_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BiocIO diff --git a/prepare/r-biocparallel/PKGBUILD b/prepare/r-biocparallel/PKGBUILD deleted file mode 100644 index 805c8c93f2..0000000000 --- a/prepare/r-biocparallel/PKGBUILD +++ /dev/null @@ -1,53 +0,0 @@ -# system requirements: C++11 -# Maintainer: Guoyi Zhang - -_pkgname=BiocParallel -_pkgver=1.28.3 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Bioconductor facilities for parallel evaluation' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') -depends=( - r - r-bh - r-futile.logger - r-snow - gcc -) -optdepends=( - r-batchjobs - r-batchtools - r-bbmisc - r-biocgenerics - r-biocstyle - r-codetools - r-data.table - r-doparallel - r-foreach - r-genomicalignments - r-genomicranges - r-knitr - r-rmpi - r-rnaseqdata.hnrnpc.bam.chr14 - r-rsamtools - r-runit - r-shortread - r-tools - r-txdb.hsapiens.ucsc.hg19.knowngene - r-variantannotation -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocparallel/lilac.py b/prepare/r-biocparallel/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biocparallel/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biocparallel/lilac.yaml b/prepare/r-biocparallel/lilac.yaml deleted file mode 100644 index 4c076999eb..0000000000 --- a/prepare/r-biocparallel/lilac.yaml +++ /dev/null @@ -1,12 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-bh -- r-futile.logger -- r-snow -update_on: -- regex: BiocParallel_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BiocParallel diff --git a/prepare/r-biomart/PKGBUILD b/prepare/r-biomart/PKGBUILD deleted file mode 100644 index ae4340696d..0000000000 --- a/prepare/r-biomart/PKGBUILD +++ /dev/null @@ -1,42 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=biomaRt -_pkgver=2.50.1 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Interface to BioMart databases (i.e. Ensembl)' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-annotationdbi - r-biocfilecache - r-digest - r-httr - r-progress - r-rappdirs - r-stringr - r-xml - r-xml2 -) -optdepends=( - r-biocstyle - r-knitr - r-mockery - r-rmarkdown - r-testthat -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomart/lilac.py b/prepare/r-biomart/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biomart/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biomart/lilac.yaml b/prepare/r-biomart/lilac.yaml deleted file mode 100644 index dfa1e059ce..0000000000 --- a/prepare/r-biomart/lilac.yaml +++ /dev/null @@ -1,18 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-annotationdbi -- r-biocfilecache -- r-digest -- r-httr -- r-progress -- r-rappdirs -- r-stringr -- r-xml -- r-xml2 -update_on: -- regex: biomaRt_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/biomaRt diff --git a/prepare/r-biostrings/PKGBUILD b/prepare/r-biostrings/PKGBUILD deleted file mode 100644 index 8f22b6d51c..0000000000 --- a/prepare/r-biostrings/PKGBUILD +++ /dev/null @@ -1,47 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=Biostrings -_pkgver=2.62.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Efficient manipulation of biological strings' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-crayon - r-genomeinfodb - r-iranges - r-s4vectors - r-xvector -) -optdepends=( - r-affy - r-affydata - r-bsgenome - r-bsgenome.celegans.ucsc.ce2 - r-bsgenome.dmelanogaster.ucsc.dm3 - r-bsgenome.hsapiens.ucsc.hg18 - r-drosophila2probe - r-genomicfeatures - r-hgu133aprobe - r-hgu95av2cdf - r-hgu95av2probe - r-rmpi - r-runit -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biostrings/lilac.py b/prepare/r-biostrings/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-biostrings/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-biostrings/lilac.yaml b/prepare/r-biostrings/lilac.yaml deleted file mode 100644 index a3e9437cf8..0000000000 --- a/prepare/r-biostrings/lilac.yaml +++ /dev/null @@ -1,15 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-crayon -- r-genomeinfodb -- r-iranges -- r-s4vectors -- r-xvector -update_on: -- regex: Biostrings_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/Biostrings diff --git a/prepare/r-bsgenome/PKGBUILD b/prepare/r-bsgenome/PKGBUILD deleted file mode 100644 index d53bbdc785..0000000000 --- a/prepare/r-bsgenome/PKGBUILD +++ /dev/null @@ -1,53 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=BSgenome -_pkgver=1.62.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Software infrastructure for efficient representation of full genomes and their SNPs' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-biostrings - r-genomeinfodb - r-genomicranges - r-iranges - r-matrixstats - r-rsamtools - r-rtracklayer - r-s4vectors - r-xvector -) -optdepends=( - r-biobase - r-biocmanager - r-bsgenome.celegans.ucsc.ce2 - r-bsgenome.hsapiens.ncbi.grch38 - r-bsgenome.hsapiens.ucsc.hg38 - r-bsgenome.hsapiens.ucsc.hg38.masked - r-bsgenome.mmusculus.ucsc.mm10 - r-bsgenome.rnorvegicus.ucsc.rn5 - r-bsgenome.scerevisiae.ucsc.saccer1 - r-hgu95av2probe - r-runit - r-snplocs.hsapiens.dbsnp144.grch38 - r-txdb.hsapiens.ucsc.hg38.knowngene - r-txdb.mmusculus.ucsc.mm10.knowngene - r-xtrasnplocs.hsapiens.dbsnp144.grch38 -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome/lilac.py b/prepare/r-bsgenome/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-bsgenome/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-bsgenome/lilac.yaml b/prepare/r-bsgenome/lilac.yaml deleted file mode 100644 index f08bbf9bf4..0000000000 --- a/prepare/r-bsgenome/lilac.yaml +++ /dev/null @@ -1,19 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-biostrings -- r-genomeinfodb -- r-genomicranges -- r-iranges -- r-matrixstats -- r-rsamtools -- r-rtracklayer -- r-s4vectors -- r-xvector -update_on: -- regex: BSgenome_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BSgenome diff --git a/prepare/r-bufferedmatrix/PKGBUILD b/prepare/r-bufferedmatrix/PKGBUILD deleted file mode 100644 index 624371eeb9..0000000000 --- a/prepare/r-bufferedmatrix/PKGBUILD +++ /dev/null @@ -1,26 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=BufferedMatrix -_pkgver=1.58.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='A matrix data storage object held in temporary files' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('LGPL') -depends=( - r -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bufferedmatrix/lilac.py b/prepare/r-bufferedmatrix/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-bufferedmatrix/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-bufferedmatrix/lilac.yaml b/prepare/r-bufferedmatrix/lilac.yaml deleted file mode 100644 index 73af77e28a..0000000000 --- a/prepare/r-bufferedmatrix/lilac.yaml +++ /dev/null @@ -1,8 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -update_on: -- regex: BufferedMatrix_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BufferedMatrix diff --git a/prepare/r-bufferedmatrixmethods/PKGBUILD b/prepare/r-bufferedmatrixmethods/PKGBUILD deleted file mode 100644 index 45a3fedc33..0000000000 --- a/prepare/r-bufferedmatrixmethods/PKGBUILD +++ /dev/null @@ -1,31 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=BufferedMatrixMethods -_pkgver=1.58.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Microarray Data related methods that utlize BufferedMatrix objects' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') -depends=( - r - r-bufferedmatrix -) -optdepends=( - r-affy - r-affyio -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bufferedmatrixmethods/lilac.py b/prepare/r-bufferedmatrixmethods/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-bufferedmatrixmethods/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-bufferedmatrixmethods/lilac.yaml b/prepare/r-bufferedmatrixmethods/lilac.yaml deleted file mode 100644 index b6b265b181..0000000000 --- a/prepare/r-bufferedmatrixmethods/lilac.yaml +++ /dev/null @@ -1,10 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-bufferedmatrix -update_on: -- regex: BufferedMatrixMethods_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/BufferedMatrixMethods diff --git a/prepare/r-delayedarray/PKGBUILD b/prepare/r-delayedarray/PKGBUILD deleted file mode 100644 index 1b65582178..0000000000 --- a/prepare/r-delayedarray/PKGBUILD +++ /dev/null @@ -1,43 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=DelayedArray -_pkgver=0.20.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='A unified framework for working transparently with on-disk and in-memory array-like datasets' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-iranges - r-matrixgenerics - r-s4vectors -) -optdepends=( - r-airway - r-biocparallel - r-biocstyle - r-delayedmatrixstats - r-genefilter - r-hdf5array - r-knitr - r-lobstr - r-rmarkdown - r-runit - r-summarizedexperiment -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delayedarray/lilac.py b/prepare/r-delayedarray/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-delayedarray/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-delayedarray/lilac.yaml b/prepare/r-delayedarray/lilac.yaml deleted file mode 100644 index f620d34a8c..0000000000 --- a/prepare/r-delayedarray/lilac.yaml +++ /dev/null @@ -1,13 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-iranges -- r-matrixgenerics -- r-s4vectors -update_on: -- regex: DelayedArray_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/DelayedArray diff --git a/prepare/r-genomeinfodb/PKGBUILD b/prepare/r-genomeinfodb/PKGBUILD deleted file mode 100644 index 932e67f4a2..0000000000 --- a/prepare/r-genomeinfodb/PKGBUILD +++ /dev/null @@ -1,45 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=GenomeInfoDb -_pkgver=1.30.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Utilities for manipulating chromosome names, including modifying them to follow a particular naming style' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-genomeinfodbdata - r-iranges - r-rcurl - r-s4vectors -) -optdepends=( - r-biocstyle - r-bsgenome - r-bsgenome.celegans.ucsc.ce2 - r-bsgenome.hsapiens.ncbi.grch38 - r-bsgenome.scerevisiae.ucsc.saccer2 - r-genomicalignments - r-genomicfeatures - r-genomicranges - r-knitr - r-rsamtools - r-runit - r-txdb.dmelanogaster.ucsc.dm3.ensgene -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomeinfodb/lilac.py b/prepare/r-genomeinfodb/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-genomeinfodb/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-genomeinfodb/lilac.yaml b/prepare/r-genomeinfodb/lilac.yaml deleted file mode 100644 index 65b280b17c..0000000000 --- a/prepare/r-genomeinfodb/lilac.yaml +++ /dev/null @@ -1,14 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-genomeinfodbdata -- r-iranges -- r-rcurl -- r-s4vectors -update_on: -- regex: GenomeInfoDb_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/GenomeInfoDb diff --git a/prepare/r-genomicalignments/PKGBUILD b/prepare/r-genomicalignments/PKGBUILD deleted file mode 100644 index 3e057979ef..0000000000 --- a/prepare/r-genomicalignments/PKGBUILD +++ /dev/null @@ -1,51 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=GenomicAlignments -_pkgver=1.30.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Representation and manipulation of short genomic alignments' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-biocparallel - r-biostrings - r-genomeinfodb - r-genomicranges - r-iranges - r-rsamtools - r-s4vectors - r-summarizedexperiment -) -optdepends=( - r-biocstyle - r-bsgenome - r-bsgenome.dmelanogaster.ucsc.dm3 - r-bsgenome.hsapiens.ucsc.hg19 - r-deseq2 - r-edger - r-genomicfeatures - r-pasillabamsubset - r-rnaseqdata.hnrnpc.bam.chr14 - r-rtracklayer - r-runit - r-shortread - r-txdb.dmelanogaster.ucsc.dm3.ensgene - r-txdb.hsapiens.ucsc.hg19.knowngene -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicalignments/lilac.py b/prepare/r-genomicalignments/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-genomicalignments/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-genomicalignments/lilac.yaml b/prepare/r-genomicalignments/lilac.yaml deleted file mode 100644 index eab3594a96..0000000000 --- a/prepare/r-genomicalignments/lilac.yaml +++ /dev/null @@ -1,18 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-biocparallel -- r-biostrings -- r-genomeinfodb -- r-genomicranges -- r-iranges -- r-rsamtools -- r-s4vectors -- r-summarizedexperiment -update_on: -- regex: GenomicAlignments_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/GenomicAlignments diff --git a/prepare/r-genomicranges/PKGBUILD b/prepare/r-genomicranges/PKGBUILD deleted file mode 100644 index 646908e7a2..0000000000 --- a/prepare/r-genomicranges/PKGBUILD +++ /dev/null @@ -1,68 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=GenomicRanges -_pkgver=1.46.1 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Representation and manipulation of genomic intervals' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-genomeinfodb - r-iranges - r-s4vectors - r-xvector -) -optdepends=( - r-annotate - r-annotationdbi - r-annotationhub - r-biobase - r-biocstyle - r-biostrings - r-bsgenome - r-bsgenome.hsapiens.ucsc.hg19 - r-bsgenome.mmusculus.ucsc.mm10 - r-bsgenome.scerevisiae.ucsc.saccer2 - r-deseq2 - r-dexseq - r-digest - r-edger - r-genomicalignments - r-genomicfeatures - r-gviz - r-hgu95av2.db - r-hgu95av2probe - r-kegggraph - r-keggrest - r-knitr - r-matrix - r-pasillabamsubset - r-rmarkdown - r-rnaseqdata.hnrnpc.bam.chr14 - r-rsamtools - r-rtracklayer - r-runit - r-summarizedexperiment - r-txdb.athaliana.biomart.plantsmart22 - r-txdb.dmelanogaster.ucsc.dm3.ensgene - r-txdb.hsapiens.ucsc.hg19.knowngene - r-txdb.mmusculus.ucsc.mm10.knowngene - r-variantannotation -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicranges/lilac.py b/prepare/r-genomicranges/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-genomicranges/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-genomicranges/lilac.yaml b/prepare/r-genomicranges/lilac.yaml deleted file mode 100644 index a0e1f0933e..0000000000 --- a/prepare/r-genomicranges/lilac.yaml +++ /dev/null @@ -1,14 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-genomeinfodb -- r-iranges -- r-s4vectors -- r-xvector -update_on: -- regex: GenomicRanges_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/GenomicRanges diff --git a/prepare/r-iranges/PKGBUILD b/prepare/r-iranges/PKGBUILD deleted file mode 100644 index c193aa6fc1..0000000000 --- a/prepare/r-iranges/PKGBUILD +++ /dev/null @@ -1,39 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=IRanges -_pkgver=2.28.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Foundation of integer range manipulation in Bioconductor' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-s4vectors -) -optdepends=( - r-biocstyle - r-bsgenome.celegans.ucsc.ce2 - r-genomicalignments - r-genomicfeatures - r-genomicranges - r-pasillabamsubset - r-rsamtools - r-runit - r-xvector -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iranges/lilac.py b/prepare/r-iranges/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-iranges/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-iranges/lilac.yaml b/prepare/r-iranges/lilac.yaml deleted file mode 100644 index cf8ba77188..0000000000 --- a/prepare/r-iranges/lilac.yaml +++ /dev/null @@ -1,11 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-s4vectors -update_on: -- regex: IRanges_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/IRanges diff --git a/prepare/r-jsonlite/PKGBUILD b/prepare/r-jsonlite/PKGBUILD deleted file mode 100644 index 75945385f8..0000000000 --- a/prepare/r-jsonlite/PKGBUILD +++ /dev/null @@ -1,37 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=jsonlite -_pkgver=1.7.2 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='A Simple and Robust JSON Parser and Generator for R' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('MIT') -depends=( - r -) -optdepends=( - r-curl - r-httr - r-knitr - r-plyr - r-r.rsp - r-rmarkdown - r-sf - r-testthat -) -source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jsonlite/lilac.py b/prepare/r-jsonlite/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-jsonlite/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-jsonlite/lilac.yaml b/prepare/r-jsonlite/lilac.yaml deleted file mode 100644 index 939bd8f891..0000000000 --- a/prepare/r-jsonlite/lilac.yaml +++ /dev/null @@ -1,8 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -update_on: -- regex: jsonlite_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=jsonlite diff --git a/prepare/r-keggrest/PKGBUILD b/prepare/r-keggrest/PKGBUILD deleted file mode 100644 index 808a3f0783..0000000000 --- a/prepare/r-keggrest/PKGBUILD +++ /dev/null @@ -1,35 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=KEGGREST -_pkgver=1.34.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biostrings - r-httr - r-png -) -optdepends=( - r-biocgenerics - r-knitr - r-markdown - r-runit -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keggrest/lilac.py b/prepare/r-keggrest/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-keggrest/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-keggrest/lilac.yaml b/prepare/r-keggrest/lilac.yaml deleted file mode 100644 index 466a95565f..0000000000 --- a/prepare/r-keggrest/lilac.yaml +++ /dev/null @@ -1,12 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biostrings -- r-httr -- r-png -update_on: -- regex: KEGGREST_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/KEGGREST diff --git a/prepare/r-matrixgenerics/PKGBUILD b/prepare/r-matrixgenerics/PKGBUILD deleted file mode 100644 index ffe32661ec..0000000000 --- a/prepare/r-matrixgenerics/PKGBUILD +++ /dev/null @@ -1,33 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=MatrixGenerics -_pkgver=1.6.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-matrixstats -) -optdepends=( - r-delayedmatrixstats - r-sparsematrixstats - r-summarizedexperiment - r-testthat -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixgenerics/lilac.py b/prepare/r-matrixgenerics/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-matrixgenerics/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-matrixgenerics/lilac.yaml b/prepare/r-matrixgenerics/lilac.yaml deleted file mode 100644 index 387bed2990..0000000000 --- a/prepare/r-matrixgenerics/lilac.yaml +++ /dev/null @@ -1,10 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-matrixstats -update_on: -- regex: MatrixGenerics_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/MatrixGenerics diff --git a/prepare/r-multtest/PKGBUILD b/prepare/r-multtest/PKGBUILD deleted file mode 100644 index 251065aec7..0000000000 --- a/prepare/r-multtest/PKGBUILD +++ /dev/null @@ -1,31 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=multtest -_pkgver=2.50.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Resampling-based multiple hypothesis testing' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('LGPL') -depends=( - r - r-biobase - r-biocgenerics -) -optdepends=( - r-snow -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multtest/lilac.py b/prepare/r-multtest/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-multtest/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-multtest/lilac.yaml b/prepare/r-multtest/lilac.yaml deleted file mode 100644 index a1478e6a64..0000000000 --- a/prepare/r-multtest/lilac.yaml +++ /dev/null @@ -1,11 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biobase -- r-biocgenerics -update_on: -- regex: multtest_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/multtest diff --git a/prepare/r-rcpp/PKGBUILD b/prepare/r-rcpp/PKGBUILD deleted file mode 100644 index c1d3251990..0000000000 --- a/prepare/r-rcpp/PKGBUILD +++ /dev/null @@ -1,32 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=Rcpp -_pkgver=1.0.7 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Seamless R and C++ Integration' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') -depends=( - r -) -optdepends=( - r-inline - r-pkgkitten - r-rbenchmark - r-tinytest -) -source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcpp/lilac.py b/prepare/r-rcpp/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-rcpp/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-rcpp/lilac.yaml b/prepare/r-rcpp/lilac.yaml deleted file mode 100644 index 32bdd7496d..0000000000 --- a/prepare/r-rcpp/lilac.yaml +++ /dev/null @@ -1,8 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -update_on: -- regex: Rcpp_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=Rcpp diff --git a/prepare/r-rhtslib/PKGBUILD b/prepare/r-rhtslib/PKGBUILD deleted file mode 100644 index 56fe79075e..0000000000 --- a/prepare/r-rhtslib/PKGBUILD +++ /dev/null @@ -1,33 +0,0 @@ -# system requirements: libbz2 & liblzma & libcurl (with header files), GNUmake -# Maintainer: Guoyi Zhang - -_pkgname=Rhtslib -_pkgver=1.26.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='HTSlib high-throughput sequencing library as an R package' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('LGPL') -depends=( - r - r-zlibbioc -) -optdepends=( - r-biocstyle - r-knitr - r-rmarkdown -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhtslib/lilac.py b/prepare/r-rhtslib/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-rhtslib/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-rhtslib/lilac.yaml b/prepare/r-rhtslib/lilac.yaml deleted file mode 100644 index 166dcd879e..0000000000 --- a/prepare/r-rhtslib/lilac.yaml +++ /dev/null @@ -1,10 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-zlibbioc -update_on: -- regex: Rhtslib_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/Rhtslib diff --git a/prepare/r-rsamtools/PKGBUILD b/prepare/r-rsamtools/PKGBUILD deleted file mode 100644 index 7bbb79660a..0000000000 --- a/prepare/r-rsamtools/PKGBUILD +++ /dev/null @@ -1,49 +0,0 @@ -# system requirements: GNU make -# Maintainer: Guoyi Zhang - -_pkgname=Rsamtools -_pkgver=2.10.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-biocparallel - r-biostrings - r-bitops - r-genomeinfodb - r-genomicranges - r-iranges - r-rhtslib - r-s4vectors - r-xvector - r-zlibbioc -) -optdepends=( - r-biocstyle - r-bsgenome.hsapiens.ucsc.hg19 - r-genomicalignments - r-genomicfeatures - r-rnaseqdata.hnrnpc.bam.chr14 - r-runit - r-shortread - r-txdb.dmelanogaster.ucsc.dm3.ensgene - r-txdb.hsapiens.ucsc.hg18.knowngene -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsamtools/lilac.py b/prepare/r-rsamtools/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-rsamtools/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-rsamtools/lilac.yaml b/prepare/r-rsamtools/lilac.yaml deleted file mode 100644 index 8cc0b2607f..0000000000 --- a/prepare/r-rsamtools/lilac.yaml +++ /dev/null @@ -1,20 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-biocparallel -- r-biostrings -- r-bitops -- r-genomeinfodb -- r-genomicranges -- r-iranges -- r-rhtslib -- r-s4vectors -- r-xvector -- r-zlibbioc -update_on: -- regex: Rsamtools_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/Rsamtools diff --git a/prepare/r-rtracklayer/PKGBUILD b/prepare/r-rtracklayer/PKGBUILD deleted file mode 100644 index eb482cab2f..0000000000 --- a/prepare/r-rtracklayer/PKGBUILD +++ /dev/null @@ -1,53 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=rtracklayer -_pkgver=1.54.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='R interface to genome annotation files and the UCSC genome browser' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-biocio - r-biostrings - r-genomeinfodb - r-genomicalignments - r-genomicranges - r-iranges - r-rcurl - r-restfulr - r-rsamtools - r-s4vectors - r-xml - r-xvector - r-zlibbioc -) -optdepends=( - r-bsgenome - r-bsgenome.hsapiens.ucsc.hg19 - r-genefilter - r-genomicfeatures - r-hgu133plus2.db - r-humanstemcell - r-limma - r-microrna - r-org.hs.eg.db - r-runit - r-txdb.hsapiens.ucsc.hg19.knowngene -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtracklayer/lilac.py b/prepare/r-rtracklayer/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-rtracklayer/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-rtracklayer/lilac.yaml b/prepare/r-rtracklayer/lilac.yaml deleted file mode 100644 index 85c20e926b..0000000000 --- a/prepare/r-rtracklayer/lilac.yaml +++ /dev/null @@ -1,23 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-biocio -- r-biostrings -- r-genomeinfodb -- r-genomicalignments -- r-genomicranges -- r-iranges -- r-rcurl -- r-restfulr -- r-rsamtools -- r-s4vectors -- r-xml -- r-xvector -- r-zlibbioc -update_on: -- regex: rtracklayer_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/rtracklayer diff --git a/prepare/r-s4vectors/PKGBUILD b/prepare/r-s4vectors/PKGBUILD deleted file mode 100644 index 217b2817e0..0000000000 --- a/prepare/r-s4vectors/PKGBUILD +++ /dev/null @@ -1,39 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=S4Vectors -_pkgver=0.32.3 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Foundation of vector-like and list-like containers in Bioconductor' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics -) -optdepends=( - r-biocstyle - r-data.table - r-delayedarray - r-genomicranges - r-graph - r-iranges - r-matrix - r-runit - r-shortread - r-summarizedexperiment -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-s4vectors/lilac.py b/prepare/r-s4vectors/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-s4vectors/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-s4vectors/lilac.yaml b/prepare/r-s4vectors/lilac.yaml deleted file mode 100644 index 3345a0088e..0000000000 --- a/prepare/r-s4vectors/lilac.yaml +++ /dev/null @@ -1,10 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -update_on: -- regex: S4Vectors_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/S4Vectors diff --git a/prepare/r-summarizedexperiment/PKGBUILD b/prepare/r-summarizedexperiment/PKGBUILD deleted file mode 100644 index fbbd9517d3..0000000000 --- a/prepare/r-summarizedexperiment/PKGBUILD +++ /dev/null @@ -1,51 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=SummarizedExperiment -_pkgver=1.24.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='SummarizedExperiment container' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biobase - r-biocgenerics - r-delayedarray - r-genomeinfodb - r-genomicranges - r-iranges - r-matrixgenerics - r-s4vectors -) -optdepends=( - r-airway - r-annotate - r-annotationdbi - r-biocstyle - r-digest - r-genomicfeatures - r-hdf5array - r-hgu95av2.db - r-jsonlite - r-knitr - r-rhdf5 - r-rmarkdown - r-runit - r-testthat - r-txdb.hsapiens.ucsc.hg19.knowngene -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-summarizedexperiment/lilac.py b/prepare/r-summarizedexperiment/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-summarizedexperiment/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-summarizedexperiment/lilac.yaml b/prepare/r-summarizedexperiment/lilac.yaml deleted file mode 100644 index 84cc3c120d..0000000000 --- a/prepare/r-summarizedexperiment/lilac.yaml +++ /dev/null @@ -1,17 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biobase -- r-biocgenerics -- r-delayedarray -- r-genomeinfodb -- r-genomicranges -- r-iranges -- r-matrixgenerics -- r-s4vectors -update_on: -- regex: SummarizedExperiment_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/SummarizedExperiment diff --git a/prepare/r-xvector/PKGBUILD b/prepare/r-xvector/PKGBUILD deleted file mode 100644 index 3dbe907197..0000000000 --- a/prepare/r-xvector/PKGBUILD +++ /dev/null @@ -1,35 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=XVector -_pkgver=0.34.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='Foundation of external vector representation and manipulation in Bioconductor' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-biocgenerics - r-iranges - r-s4vectors - r-zlibbioc -) -optdepends=( - r-biostrings - r-drosophila2probe - r-runit -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xvector/lilac.py b/prepare/r-xvector/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-xvector/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-xvector/lilac.yaml b/prepare/r-xvector/lilac.yaml deleted file mode 100644 index b4c747a2a0..0000000000 --- a/prepare/r-xvector/lilac.yaml +++ /dev/null @@ -1,13 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -repo_depends: -- r-biocgenerics -- r-iranges -- r-s4vectors -- r-zlibbioc -update_on: -- regex: XVector_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/XVector diff --git a/prepare/r-zlibbioc/PKGBUILD b/prepare/r-zlibbioc/PKGBUILD deleted file mode 100644 index 08f4f50d73..0000000000 --- a/prepare/r-zlibbioc/PKGBUILD +++ /dev/null @@ -1,26 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=zlibbioc -_pkgver=1.40.0 -pkgname=r-${_pkgname,,} -pkgver=${_pkgver//[:-]/.} -pkgrel=1 -pkgdesc='An R packaged zlib-1.2.5' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') -depends=( - r -) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a') - -build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" -} - -package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -} -# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zlibbioc/lilac.py b/prepare/r-zlibbioc/lilac.py deleted file mode 100644 index 620556bc87..0000000000 --- a/prepare/r-zlibbioc/lilac.py +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() diff --git a/prepare/r-zlibbioc/lilac.yaml b/prepare/r-zlibbioc/lilac.yaml deleted file mode 100644 index a74259d6d2..0000000000 --- a/prepare/r-zlibbioc/lilac.yaml +++ /dev/null @@ -1,8 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: starsareintherose@outlook.com -update_on: -- regex: zlibbioc_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/zlibbioc