From 26152685efff7fe6e6a82589502dc994b5046a25 Mon Sep 17 00:00:00 2001 From: Pekka Ristola Date: Fri, 16 Feb 2024 17:51:20 +0200 Subject: [PATCH] r-*: delete R packages that were removed from CRAN and Bioconductor See #197 --- BioArchLinux/r-aspediafi/PKGBUILD | 53 -------------------------- BioArchLinux/r-aspediafi/lilac.py | 13 ------- BioArchLinux/r-aspediafi/lilac.yaml | 34 ----------------- BioArchLinux/r-copywriter/PKGBUILD | 45 ---------------------- BioArchLinux/r-copywriter/lilac.py | 13 ------- BioArchLinux/r-copywriter/lilac.yaml | 24 ------------ BioArchLinux/r-epihet/PKGBUILD | 47 ----------------------- BioArchLinux/r-epihet/lilac.py | 13 ------- BioArchLinux/r-epihet/lilac.yaml | 24 ------------ BioArchLinux/r-genotypeeval/PKGBUILD | 41 -------------------- BioArchLinux/r-genotypeeval/lilac.py | 13 ------- BioArchLinux/r-genotypeeval/lilac.yaml | 18 --------- BioArchLinux/r-metavizr/PKGBUILD | 51 ------------------------- BioArchLinux/r-metavizr/lilac.py | 13 ------- BioArchLinux/r-metavizr/lilac.yaml | 22 ----------- BioArchLinux/r-optimr/PKGBUILD | 35 ----------------- BioArchLinux/r-optimr/lilac.py | 13 ------- BioArchLinux/r-optimr/lilac.yaml | 15 -------- BioArchLinux/r-perturbatr/PKGBUILD | 52 ------------------------- BioArchLinux/r-perturbatr/lilac.py | 13 ------- BioArchLinux/r-perturbatr/lilac.yaml | 25 ------------ BioArchLinux/r-profia/PKGBUILD | 38 ------------------ BioArchLinux/r-profia/lilac.py | 13 ------- BioArchLinux/r-profia/lilac.yaml | 17 --------- BioArchLinux/r-stan/PKGBUILD | 39 ------------------- BioArchLinux/r-stan/lilac.py | 13 ------- BioArchLinux/r-stan/lilac.yaml | 18 --------- BioArchLinux/r-tarseqqc/PKGBUILD | 45 ---------------------- BioArchLinux/r-tarseqqc/lilac.py | 13 ------- BioArchLinux/r-tarseqqc/lilac.yaml | 25 ------------ BioArchLinux/r-uchardet/PKGBUILD | 32 ---------------- BioArchLinux/r-uchardet/lilac.py | 13 ------- BioArchLinux/r-uchardet/lilac.yaml | 9 ----- 33 files changed, 852 deletions(-) delete mode 100644 BioArchLinux/r-aspediafi/PKGBUILD delete mode 100644 BioArchLinux/r-aspediafi/lilac.py delete mode 100644 BioArchLinux/r-aspediafi/lilac.yaml delete mode 100644 BioArchLinux/r-copywriter/PKGBUILD delete mode 100644 BioArchLinux/r-copywriter/lilac.py delete mode 100644 BioArchLinux/r-copywriter/lilac.yaml delete mode 100644 BioArchLinux/r-epihet/PKGBUILD delete mode 100644 BioArchLinux/r-epihet/lilac.py delete mode 100644 BioArchLinux/r-epihet/lilac.yaml delete mode 100644 BioArchLinux/r-genotypeeval/PKGBUILD delete mode 100644 BioArchLinux/r-genotypeeval/lilac.py delete mode 100644 BioArchLinux/r-genotypeeval/lilac.yaml delete mode 100644 BioArchLinux/r-metavizr/PKGBUILD delete mode 100644 BioArchLinux/r-metavizr/lilac.py delete mode 100644 BioArchLinux/r-metavizr/lilac.yaml delete mode 100644 BioArchLinux/r-optimr/PKGBUILD delete mode 100644 BioArchLinux/r-optimr/lilac.py delete mode 100644 BioArchLinux/r-optimr/lilac.yaml delete mode 100644 BioArchLinux/r-perturbatr/PKGBUILD delete mode 100644 BioArchLinux/r-perturbatr/lilac.py delete mode 100644 BioArchLinux/r-perturbatr/lilac.yaml delete mode 100644 BioArchLinux/r-profia/PKGBUILD delete mode 100644 BioArchLinux/r-profia/lilac.py delete mode 100644 BioArchLinux/r-profia/lilac.yaml delete mode 100644 BioArchLinux/r-stan/PKGBUILD delete mode 100644 BioArchLinux/r-stan/lilac.py delete mode 100644 BioArchLinux/r-stan/lilac.yaml delete mode 100644 BioArchLinux/r-tarseqqc/PKGBUILD delete mode 100644 BioArchLinux/r-tarseqqc/lilac.py delete mode 100644 BioArchLinux/r-tarseqqc/lilac.yaml delete mode 100644 BioArchLinux/r-uchardet/PKGBUILD delete mode 100644 BioArchLinux/r-uchardet/lilac.py delete mode 100644 BioArchLinux/r-uchardet/lilac.yaml diff --git a/BioArchLinux/r-aspediafi/PKGBUILD b/BioArchLinux/r-aspediafi/PKGBUILD deleted file mode 100644 index 47fbae8e20..0000000000 --- a/BioArchLinux/r-aspediafi/PKGBUILD +++ /dev/null @@ -1,53 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=ASpediaFI -_pkgver=1.11.0 -pkgname=r-${_pkgname,,} -pkgver=1.11.0 -pkgrel=3 -pkgdesc='ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events' -arch=('any') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('GPL') -depends=( - r - r-biocparallel - r-biomart - r-dplyr - r-drawr - r-e1071 - r-fgsea - r-genomeinfodb - r-genomicalignments - r-genomicfeatures - r-genomicranges - r-ggplot2 - r-gviz - r-igraph - r-iranges - r-ivas - r-limma - r-mgsz - r-reshape2 - r-rocr - r-rsamtools - r-rtracklayer - r-s4vectors - r-scales - r-summarizedexperiment -) -optdepends=( - r-knitr -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('bada73c70b81c82b88bd2a014b01d05a1eedde536a9df19311ae41a498f1568e') - -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/BioArchLinux/r-aspediafi/lilac.py b/BioArchLinux/r-aspediafi/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-aspediafi/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-aspediafi/lilac.yaml b/BioArchLinux/r-aspediafi/lilac.yaml deleted file mode 100644 index 872b41331f..0000000000 --- a/BioArchLinux/r-aspediafi/lilac.yaml +++ /dev/null @@ -1,34 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biocparallel -- r-biomart -- r-dplyr -- r-drawr -- r-e1071 -- r-fgsea -- r-genomeinfodb -- r-genomicalignments -- r-genomicfeatures -- r-genomicranges -- r-ggplot2 -- r-gviz -- r-igraph -- r-iranges -- r-ivas -- r-limma -- r-mgsz -- r-reshape2 -- r-rocr -- r-rsamtools -- r-rtracklayer -- r-s4vectors -- r-scales -- r-summarizedexperiment -update_on: -- regex: ASpediaFI_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/ASpediaFI -- alias: r diff --git a/BioArchLinux/r-copywriter/PKGBUILD b/BioArchLinux/r-copywriter/PKGBUILD deleted file mode 100644 index 45f80f25d7..0000000000 --- a/BioArchLinux/r-copywriter/PKGBUILD +++ /dev/null @@ -1,45 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=CopywriteR -_pkgver=2.29.0 -pkgname=r-${_pkgname,,} -pkgver=2.29.0 -pkgrel=3 -pkgdesc='Copy number information from targeted sequencing using off-target reads' -arch=('any') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('GPL') -depends=( - r - r-biocparallel - r-chipseq - r-copyhelper - r-data.table - r-dnacopy - r-futile.logger - r-genomeinfodb - r-genomicalignments - r-genomicranges - r-gtools - r-iranges - r-matrixstats - r-rsamtools - r-s4vectors -) -optdepends=( - r-biocstyle - r-sclcbam - r-snow -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('46f7f6918a01b13de3f730057c19c9e9bb8594df34c5ef1399efabc665f68cc0') - -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/BioArchLinux/r-copywriter/lilac.py b/BioArchLinux/r-copywriter/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-copywriter/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-copywriter/lilac.yaml b/BioArchLinux/r-copywriter/lilac.yaml deleted file mode 100644 index 8ff8a4f28c..0000000000 --- a/BioArchLinux/r-copywriter/lilac.yaml +++ /dev/null @@ -1,24 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biocparallel -- r-chipseq -- r-copyhelper -- r-data.table -- r-dnacopy -- r-futile.logger -- r-genomeinfodb -- r-genomicalignments -- r-genomicranges -- r-gtools -- r-iranges -- r-matrixstats -- r-rsamtools -- r-s4vectors -update_on: -- regex: CopywriteR_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/CopywriteR -- alias: r diff --git a/BioArchLinux/r-epihet/PKGBUILD b/BioArchLinux/r-epihet/PKGBUILD deleted file mode 100644 index 5b9e237bc8..0000000000 --- a/BioArchLinux/r-epihet/PKGBUILD +++ /dev/null @@ -1,47 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=epihet -_pkgver=1.13.0 -pkgname=r-${_pkgname,,} -pkgver=1.13.0 -pkgrel=3 -pkgdesc='Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data' -arch=('any') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('Artistic2.0') -depends=( - r - r-data.table - r-doparallel - r-entropyexplorer - r-foreach - r-genomicranges - r-ggplot2 - r-igraph - r-iranges - r-pheatmap - r-qvalue - r-reactomepa - r-rtsne - r-s4vectors - r-wgcna -) -optdepends=( - r-clusterprofiler - r-ggfortify - r-knitr - r-org.hs.eg.db - r-rmarkdown -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('f928a39240a5e5a7de7d75b15fa2da62d01b3e6c276cb01d80467a34c87abadc') - -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/BioArchLinux/r-epihet/lilac.py b/BioArchLinux/r-epihet/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-epihet/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-epihet/lilac.yaml b/BioArchLinux/r-epihet/lilac.yaml deleted file mode 100644 index 70a6a1cae6..0000000000 --- a/BioArchLinux/r-epihet/lilac.yaml +++ /dev/null @@ -1,24 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-data.table -- r-doparallel -- r-entropyexplorer -- r-foreach -- r-genomicranges -- r-ggplot2 -- r-igraph -- r-iranges -- r-pheatmap -- r-qvalue -- r-reactomepa -- r-rtsne -- r-s4vectors -- r-wgcna -update_on: -- regex: epihet_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/epihet -- alias: r diff --git a/BioArchLinux/r-genotypeeval/PKGBUILD b/BioArchLinux/r-genotypeeval/PKGBUILD deleted file mode 100644 index 5c04092cb0..0000000000 --- a/BioArchLinux/r-genotypeeval/PKGBUILD +++ /dev/null @@ -1,41 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=genotypeeval -_pkgver=1.30.0 -pkgname=r-${_pkgname,,} -pkgver=1.30.0 -pkgrel=3 -pkgdesc='QA/QC of a gVCF or VCF file' -arch=('any') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('custom') -depends=( - r - r-biocgenerics - r-biocparallel - r-genomeinfodb - r-genomicranges - r-ggplot2 - r-iranges - r-rtracklayer - r-variantannotation -) -optdepends=( - r-rmarkdown - r-snplocs.hsapiens.dbsnp141.grch38 - r-testthat - r-txdb.hsapiens.ucsc.hg38.knowngene -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('d4e2b92ddf1cb7f72cb131c05575fefa161d8c4527f9afb9530f6d120d6a2156') - -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/${pkgname}" -} -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-genotypeeval/lilac.py b/BioArchLinux/r-genotypeeval/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-genotypeeval/lilac.py +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() - update_aur_repo() diff --git a/BioArchLinux/r-genotypeeval/lilac.yaml b/BioArchLinux/r-genotypeeval/lilac.yaml deleted file mode 100644 index a449474f75..0000000000 --- a/BioArchLinux/r-genotypeeval/lilac.yaml +++ /dev/null @@ -1,18 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biocgenerics -- r-biocparallel -- r-genomeinfodb -- r-genomicranges -- r-ggplot2 -- r-iranges -- r-rtracklayer -- r-variantannotation -update_on: -- regex: genotypeeval_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/genotypeeval -- alias: r diff --git a/BioArchLinux/r-metavizr/PKGBUILD b/BioArchLinux/r-metavizr/PKGBUILD deleted file mode 100644 index 6ed30cd15e..0000000000 --- a/BioArchLinux/r-metavizr/PKGBUILD +++ /dev/null @@ -1,51 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=metavizr -_pkgver=1.21.0 -pkgname=r-${_pkgname,,} -pkgver=1.21.0 -pkgrel=3 -pkgdesc='R Interface to the metaviz web app for interactive metagenomics data analysis and visualization' -arch=('any') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('MIT') -depends=( - r - r-biobase - r-data.table - r-digest - r-epivizr - r-epivizrdata - r-epivizrserver - r-epivizrstandalone - r-genomeinfodb - r-httr - r-metagenomeseq - r-phyloseq - r-vegan -) -optdepends=( - r-biocstyle - r-etec16s - r-experimenthub - r-gss - r-knitr - r-matrixstats - r-msd16s - r-rmarkdown - r-testthat - r-tidyr -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('bac67d6bc05818abd6bfaffc6969b74a7e5f00ae737b4de715b5584d0a7208b5') - -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/${pkgname}" -} -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-metavizr/lilac.py b/BioArchLinux/r-metavizr/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-metavizr/lilac.py +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env python3 -from lilaclib import * - -def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) - -def post_build(): - git_pkgbuild_commit() - update_aur_repo() diff --git a/BioArchLinux/r-metavizr/lilac.yaml b/BioArchLinux/r-metavizr/lilac.yaml deleted file mode 100644 index bd6f13aaa3..0000000000 --- a/BioArchLinux/r-metavizr/lilac.yaml +++ /dev/null @@ -1,22 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biobase -- r-data.table -- r-digest -- r-epivizr -- r-epivizrdata -- r-epivizrserver -- r-epivizrstandalone -- r-genomeinfodb -- r-httr -- r-metagenomeseq -- r-phyloseq -- r-vegan -update_on: -- regex: metavizr_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/metavizr -- alias: r diff --git a/BioArchLinux/r-optimr/PKGBUILD b/BioArchLinux/r-optimr/PKGBUILD deleted file mode 100644 index fa6e102399..0000000000 --- a/BioArchLinux/r-optimr/PKGBUILD +++ /dev/null @@ -1,35 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=optimr -_pkgver=2019-12.16 -pkgname=r-${_pkgname,,} -pkgver=2019.12.16 -pkgrel=6 -pkgdesc="A Replacement and Extension of the 'optim' Function" -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') -depends=( - r - r-numderiv - r-optextras - r-rcgmin - r-rvmmin - r-setrng -) -optdepends=( - r-knitr - r-rmarkdown -) -source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00') - -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/BioArchLinux/r-optimr/lilac.py b/BioArchLinux/r-optimr/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-optimr/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-optimr/lilac.yaml b/BioArchLinux/r-optimr/lilac.yaml deleted file mode 100644 index 23dc8af680..0000000000 --- a/BioArchLinux/r-optimr/lilac.yaml +++ /dev/null @@ -1,15 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-numderiv -- r-optextras -- r-rcgmin -- r-rvmmin -- r-setrng -update_on: -- regex: optimr_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=optimr -- alias: r diff --git a/BioArchLinux/r-perturbatr/PKGBUILD b/BioArchLinux/r-perturbatr/PKGBUILD deleted file mode 100644 index 47a39e5555..0000000000 --- a/BioArchLinux/r-perturbatr/PKGBUILD +++ /dev/null @@ -1,52 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=perturbatr -_pkgver=1.16.0 -pkgname=r-${_pkgname,,} -pkgver=1.16.0 -pkgrel=5 -pkgdesc='Statistical Analysis of High-Throughput Genetic Perturbation Screens' -arch=('any') -url="https://bioconductor.org/packages/3.15/${_pkgname}" -license=('GPL') -depends=( - r - r-assertthat - r-diffusr - r-doparallel - r-dplyr - r-foreach - r-formula.tools - r-ggplot2 - r-igraph - r-lazyeval - r-lme4 - r-magrittr - r-rlang - r-scales - r-tibble - r-tidyr -) -optdepends=( - r-biocstyle - r-knitr - r-lintr - r-rmarkdown - r-testthat -) -makedepends=( - git -) -source=("git+https://git.bioconductor.org/packages/${_pkgname}") -sha256sums=('SKIP') - -build() { - tar -zcvf ${_pkgname}_${_pkgver}.tar.gz ${_pkgname} - 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/BioArchLinux/r-perturbatr/lilac.py b/BioArchLinux/r-perturbatr/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-perturbatr/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-perturbatr/lilac.yaml b/BioArchLinux/r-perturbatr/lilac.yaml deleted file mode 100644 index 213cd8c809..0000000000 --- a/BioArchLinux/r-perturbatr/lilac.yaml +++ /dev/null @@ -1,25 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-assertthat -- r-diffusr -- r-doparallel -- r-dplyr -- r-foreach -- r-formula.tools -- r-ggplot2 -- r-igraph -- r-lazyeval -- r-lme4 -- r-magrittr -- r-rlang -- r-scales -- r-tibble -- r-tidyr -update_on: -- regex: (\d+.\d+.\d+) - source: regex - url: https://bioconductor.org/packages/3.15/perturbatr -- alias: r diff --git a/BioArchLinux/r-profia/PKGBUILD b/BioArchLinux/r-profia/PKGBUILD deleted file mode 100644 index ecc6e684ec..0000000000 --- a/BioArchLinux/r-profia/PKGBUILD +++ /dev/null @@ -1,38 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=proFIA -_pkgver=1.23.0 -pkgname=r-${_pkgname,,} -pkgver=1.23.0 -pkgrel=3 -pkgdesc='Preprocessing of FIA-HRMS data' -arch=('x86_64') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('CeCILL') -depends=( - r - r-biobase - r-biocparallel - r-minpack.lm - r-missforest - r-pracma - r-ropls - r-xcms -) -optdepends=( - r-biocgenerics - r-knitr - r-plasfia -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('723bb21f11cfa9366f8ec1a229290f3383b621495d72d9df6e85b80088dc0878') - -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/BioArchLinux/r-profia/lilac.py b/BioArchLinux/r-profia/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-profia/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-profia/lilac.yaml b/BioArchLinux/r-profia/lilac.yaml deleted file mode 100644 index f517edc654..0000000000 --- a/BioArchLinux/r-profia/lilac.yaml +++ /dev/null @@ -1,17 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biobase -- r-biocparallel -- r-minpack.lm -- r-missforest -- r-pracma -- r-ropls -- r-xcms -update_on: -- regex: proFIA_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/proFIA -- alias: r diff --git a/BioArchLinux/r-stan/PKGBUILD b/BioArchLinux/r-stan/PKGBUILD deleted file mode 100644 index 6495bdd6ac..0000000000 --- a/BioArchLinux/r-stan/PKGBUILD +++ /dev/null @@ -1,39 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=STAN -_pkgver=2.26.2 -pkgname=r-${_pkgname,,} -pkgver=2.26.2 -pkgrel=2 -pkgdesc='The Genomic STate ANnotation Package' -arch=('x86_64') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('GPL') -depends=( - r - r-biocgenerics - r-genomeinfodb - r-genomicranges - r-gviz - r-iranges - r-poilog - r-rsolnp - r-s4vectors -) -optdepends=( - r-biocstyle - r-gplots - r-knitr -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('7b72748cb5e42f99f96eb34314230c3f047324d592680fb6c9762f15c582a435') - -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/BioArchLinux/r-stan/lilac.py b/BioArchLinux/r-stan/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-stan/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-stan/lilac.yaml b/BioArchLinux/r-stan/lilac.yaml deleted file mode 100644 index 18ea917ce4..0000000000 --- a/BioArchLinux/r-stan/lilac.yaml +++ /dev/null @@ -1,18 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biocgenerics -- r-genomeinfodb -- r-genomicranges -- r-gviz -- r-iranges -- r-poilog -- r-rsolnp -- r-s4vectors -update_on: -- regex: STAN_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/STAN -- alias: r diff --git a/BioArchLinux/r-tarseqqc/PKGBUILD b/BioArchLinux/r-tarseqqc/PKGBUILD deleted file mode 100644 index ad8b32c8c5..0000000000 --- a/BioArchLinux/r-tarseqqc/PKGBUILD +++ /dev/null @@ -1,45 +0,0 @@ -# Maintainer: Guoyi Zhang - -_pkgname=TarSeqQC -_pkgver=1.28.0 -pkgname=r-${_pkgname,,} -pkgver=1.28.0 -pkgrel=3 -pkgdesc='TARgeted SEQuencing Experiment Quality Control' -arch=('any') -url="https://bioconductor.org/packages/3.17/${_pkgname}" -license=('GPL') -depends=( - r - r-biocgenerics - r-biocparallel - r-biostrings - r-cowplot - r-genomeinfodb - r-genomicalignments - r-genomicranges - r-ggplot2 - r-hmisc - r-iranges - r-openxlsx - r-plyr - r-reshape2 - r-rsamtools - r-s4vectors -) -optdepends=( - r-biocmanager - r-runit -) -source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('65c8426620a3cede237452b3ff7bb84577a90e364fdb06e7a521ad563d523592') - -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/BioArchLinux/r-tarseqqc/lilac.py b/BioArchLinux/r-tarseqqc/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-tarseqqc/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-tarseqqc/lilac.yaml b/BioArchLinux/r-tarseqqc/lilac.yaml deleted file mode 100644 index 391f754080..0000000000 --- a/BioArchLinux/r-tarseqqc/lilac.yaml +++ /dev/null @@ -1,25 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -repo_depends: -- r-biocgenerics -- r-biocparallel -- r-biostrings -- r-cowplot -- r-genomeinfodb -- r-genomicalignments -- r-genomicranges -- r-ggplot2 -- r-hmisc -- r-iranges -- r-openxlsx -- r-plyr -- r-reshape2 -- r-rsamtools -- r-s4vectors -update_on: -- regex: TarSeqQC_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/3.17/TarSeqQC -- alias: r diff --git a/BioArchLinux/r-uchardet/PKGBUILD b/BioArchLinux/r-uchardet/PKGBUILD deleted file mode 100644 index 6f1502c2bb..0000000000 --- a/BioArchLinux/r-uchardet/PKGBUILD +++ /dev/null @@ -1,32 +0,0 @@ -# system requirements: C++11, GNU make -# Maintainer: Guoyi Zhang - -_pkgname=uchardet -_pkgver=1.1.1 -pkgname=r-${_pkgname,,} -pkgver=1.1.1 -pkgrel=4 -pkgdesc='The Universal Character Encoding Detector' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') -depends=( - r -) -optdepends=( - r-knitr - r-rmarkdown - r-tinytest -) -source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('b23129aa6a8abdfb7118e8b469abdb9e4a3a1ccb9ca50627ec0d577d00f27d54') - -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/BioArchLinux/r-uchardet/lilac.py b/BioArchLinux/r-uchardet/lilac.py deleted file mode 100644 index bd219c037c..0000000000 --- a/BioArchLinux/r-uchardet/lilac.py +++ /dev/null @@ -1,13 +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() - update_aur_repo() diff --git a/BioArchLinux/r-uchardet/lilac.yaml b/BioArchLinux/r-uchardet/lilac.yaml deleted file mode 100644 index fb910c89d9..0000000000 --- a/BioArchLinux/r-uchardet/lilac.yaml +++ /dev/null @@ -1,9 +0,0 @@ -build_prefix: extra-x86_64 -maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org -update_on: -- regex: uchardet_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=uchardet -- alias: r