diff --git a/BioArchLinux/r-iaseq/PKGBUILD b/BioArchLinux/r-iaseq/PKGBUILD index b3e3653260..0895d86a72 100644 --- a/BioArchLinux/r-iaseq/PKGBUILD +++ b/BioArchLinux/r-iaseq/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=iASeq _pkgver=1.46.0 pkgname=r-${_pkgname,,} -pkgver=1.46.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='iASeq: integrating multiple sequencing datasets for detecting allele-specific events' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="integrating multiple sequencing datasets for detecting allele-specific events" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-only') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('35f0563d9c1573290e1e726ff16099c580239e11c13577a39632e59634c29478') +md5sums=('3086632b16254c5b1f22c4f376bd43a7') +b2sums=('9c61497d515671c501d808184d8d64e6ef5d204f6d6ea24e25f4e36d8004dde49cbfadcdd62aa63122041035e9907e56876304f05b7b92dba579e527d5a800e9') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-iaseq/lilac.py b/BioArchLinux/r-iaseq/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-iaseq/lilac.py +++ b/BioArchLinux/r-iaseq/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-iaseq/lilac.yaml b/BioArchLinux/r-iaseq/lilac.yaml index 7290bf475f..b7f463923f 100644 --- a/BioArchLinux/r-iaseq/lilac.yaml +++ b/BioArchLinux/r-iaseq/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: iASeq_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/iASeq +- source: rpkgs + pkgname: iASeq + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-iclusterplus/PKGBUILD b/BioArchLinux/r-iclusterplus/PKGBUILD index db886aba1c..203918c919 100644 --- a/BioArchLinux/r-iclusterplus/PKGBUILD +++ b/BioArchLinux/r-iclusterplus/PKGBUILD @@ -3,31 +3,34 @@ _pkgname=iClusterPlus _pkgver=1.38.0 pkgname=r-${_pkgname,,} -pkgver=1.38.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Integrative clustering of multi-type genomic data' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Integrative clustering of multi-type genomic data" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( + blas + lapack r ) +makedepends=( + gcc-fortran +) optdepends=( r-biocgenerics r-runit ) -makedepends=( - gcc-fortran -) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('414f66fd6513a6563a7b219b6e3055276fc6a68f7e36134810e9c93088e1a65c') +md5sums=('133b682823ec6ab41f6f6579413d461d') +b2sums=('3d21f898f84ead21e97fbabe5ef0219a692097263c3710a98d58110278ba04d8d4131671a886c3cc3a570894a8e22a1baf45d8eed331c91ddf25d4fc7de7f0c3') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-iclusterplus/lilac.py b/BioArchLinux/r-iclusterplus/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-iclusterplus/lilac.py +++ b/BioArchLinux/r-iclusterplus/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-iclusterplus/lilac.yaml b/BioArchLinux/r-iclusterplus/lilac.yaml index a9edd12adc..d0a08d6cd6 100644 --- a/BioArchLinux/r-iclusterplus/lilac.yaml +++ b/BioArchLinux/r-iclusterplus/lilac.yaml @@ -3,7 +3,16 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: iClusterPlus_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/iClusterPlus +- source: rpkgs + pkgname: iClusterPlus + repo: bioc + md5: true - alias: r +- source: alpmfiles + pkgname: blas + filename: usr/lib/libblas\.so\.([^.]+) + repo: extra +- source: alpmfiles + pkgname: lapack + filename: usr/lib/liblapack\.so\.([^.]+) + repo: extra diff --git a/BioArchLinux/r-iseq/PKGBUILD b/BioArchLinux/r-iseq/PKGBUILD index d7ceff394b..a4e7d142ae 100644 --- a/BioArchLinux/r-iseq/PKGBUILD +++ b/BioArchLinux/r-iseq/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=iSeq _pkgver=1.54.0 pkgname=r-${_pkgname,,} -pkgver=1.54.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('2f0f4845e0e5a25a1cf14c7209b833e85d0541f8f9986978c2946e2f0bed86d5') +md5sums=('1798c4c248175516afc66ee7f45d5051') +b2sums=('bdefae2fd5cce0aee3203bc2d3969e944ba515b2dfaca503970707c5a1b5f43a0bff27cd5a23ed13fd992565d71448674af6975e4e7f3f46dee51164d59646b6') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-iseq/lilac.py b/BioArchLinux/r-iseq/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-iseq/lilac.py +++ b/BioArchLinux/r-iseq/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-iseq/lilac.yaml b/BioArchLinux/r-iseq/lilac.yaml index a2016bce77..3b8be2479a 100644 --- a/BioArchLinux/r-iseq/lilac.yaml +++ b/BioArchLinux/r-iseq/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: iSeq_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/iSeq +- source: rpkgs + pkgname: iSeq + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-isolde/PKGBUILD b/BioArchLinux/r-isolde/PKGBUILD index c2f5b47216..b64a8f53e8 100644 --- a/BioArchLinux/r-isolde/PKGBUILD +++ b/BioArchLinux/r-isolde/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=ISoLDE _pkgver=1.30.0 pkgname=r-${_pkgname,,} -pkgver=1.30.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Integrative Statistics of alleLe Dependent Expression' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Integrative Statistics of alleLe Dependent Expression" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('edbace394f931c0257a5c4e500be696a13183c30c1fa2383130808dd7ccb1dad') +md5sums=('448414b250ff7c903395638de3688411') +b2sums=('bcb63ed3ab162c5d194a2f4470cb9fc455a295dafdeaacfdae0ff24fda7c6278c9684873ecada6249d44ee45afe7d87a295e7de351b00c84029043bc14c9cf59') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-isolde/lilac.py b/BioArchLinux/r-isolde/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-isolde/lilac.py +++ b/BioArchLinux/r-isolde/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-isolde/lilac.yaml b/BioArchLinux/r-isolde/lilac.yaml index 3147aae66c..6bc457de74 100644 --- a/BioArchLinux/r-isolde/lilac.yaml +++ b/BioArchLinux/r-isolde/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: ISoLDE_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/ISoLDE +- source: rpkgs + pkgname: ISoLDE + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-kboost/PKGBUILD b/BioArchLinux/r-kboost/PKGBUILD index 2cfdea2d2d..fbeeb43806 100644 --- a/BioArchLinux/r-kboost/PKGBUILD +++ b/BioArchLinux/r-kboost/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=KBoost _pkgver=1.10.0 pkgname=r-${_pkgname,,} -pkgver=1.10.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Inference of gene regulatory networks from gene expression data' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Inference of gene regulatory networks from gene expression data" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-only OR GPL-3.0-only') depends=( r ) @@ -18,14 +18,15 @@ optdepends=( r-testthat ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('1132da444f04934200dd92483b478116c51d9a995b698648e88b97b109086de9') +md5sums=('853c93af3367a8af56b60aea8495f44b') +b2sums=('90e22d4770056298a98d2554cdf6cfaf5918d971e6ddbb96ea1b0e7cf21666c2e5a0cc4fd50a4d3708bc6489fe7dba9268a0df25bebd0772dab6d076ccdef0a5') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-kboost/lilac.py b/BioArchLinux/r-kboost/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-kboost/lilac.py +++ b/BioArchLinux/r-kboost/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-kboost/lilac.yaml b/BioArchLinux/r-kboost/lilac.yaml index b11ed16031..58241d35df 100644 --- a/BioArchLinux/r-kboost/lilac.yaml +++ b/BioArchLinux/r-kboost/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: KBoost_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/KBoost +- source: rpkgs + pkgname: KBoost + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-lbe/PKGBUILD b/BioArchLinux/r-lbe/PKGBUILD index e3e17f5cee..0f34c478dd 100644 --- a/BioArchLinux/r-lbe/PKGBUILD +++ b/BioArchLinux/r-lbe/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=LBE _pkgver=1.70.0 pkgname=r-${_pkgname,,} -pkgver=1.70.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Estimation of the false discovery rate.' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Estimation of the false discovery rate" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-only') depends=( r ) @@ -16,14 +16,15 @@ optdepends=( r-qvalue ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('99990d21cff0a2b427afbade12547c637c5aeb63a494f956b6d6f0d97a7e723b') +md5sums=('36559f365f1dbd53056e6b43bc1e06e9') +b2sums=('8c10241e146be6fc61c48ba4ac7e6a7b4691c5499a89d920c9b64e7c5a1729a2d3ed5d265a853402b247427fe2ad4e0d8f789bc70fd504695d1673da7006439a') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-lbe/lilac.py b/BioArchLinux/r-lbe/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-lbe/lilac.py +++ b/BioArchLinux/r-lbe/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-lbe/lilac.yaml b/BioArchLinux/r-lbe/lilac.yaml index 70a0854754..843d0c29ea 100644 --- a/BioArchLinux/r-lbe/lilac.yaml +++ b/BioArchLinux/r-lbe/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: LBE_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/LBE +- source: rpkgs + pkgname: LBE + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-lea/PKGBUILD b/BioArchLinux/r-lea/PKGBUILD index 76ab8e1dbf..8ebc4069ba 100644 --- a/BioArchLinux/r-lea/PKGBUILD +++ b/BioArchLinux/r-lea/PKGBUILD @@ -3,27 +3,29 @@ _pkgname=LEA _pkgver=3.14.0 pkgname=r-${_pkgname,,} -pkgver=3.14.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='LEA: an R package for Landscape and Ecological Association Studies' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="an R package for Landscape and Ecological Association Studies" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( + lapack r ) optdepends=( r-knitr ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('611918debc6f25f2cc7277f77979a3e8352c517b63bea56626c6fd9c2ecb14e6') +md5sums=('e32cbc2a97921f9b911eef1a5d1ef3d7') +b2sums=('6c39d143ccc7213006f7fca3221ecef3aff81957cce5999c3e417cb007afb011ff54c90701a80dbd4d7e6671f86a8cf03575a154186b3765dd57bce68737fee9') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-lea/lilac.py b/BioArchLinux/r-lea/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-lea/lilac.py +++ b/BioArchLinux/r-lea/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-lea/lilac.yaml b/BioArchLinux/r-lea/lilac.yaml index 380b98dc59..08036ab4b6 100644 --- a/BioArchLinux/r-lea/lilac.yaml +++ b/BioArchLinux/r-lea/lilac.yaml @@ -3,7 +3,12 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: LEA_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/LEA +- source: rpkgs + pkgname: LEA + repo: bioc + md5: true - alias: r +- source: alpmfiles + pkgname: lapack + filename: usr/lib/liblapack\.so\.([^.]+) + repo: extra diff --git a/BioArchLinux/r-macorrplot/PKGBUILD b/BioArchLinux/r-macorrplot/PKGBUILD index d3dd6996f6..7d90a89349 100644 --- a/BioArchLinux/r-macorrplot/PKGBUILD +++ b/BioArchLinux/r-macorrplot/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=maCorrPlot _pkgver=1.72.0 pkgname=r-${_pkgname,,} -pkgver=1.72.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Visualize artificial correlation in microarray data' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Visualize artificial correlation in microarray data" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('eb8ecf43408aca3669ffdb109f4d4bedf3962cb08760ff27a68d6ceb5226f23e') +md5sums=('4d4be51b04e4ff3e09aff6643eeed215') +b2sums=('1739fc5d560b984619dcb71eba5d631aba3c5b471c42643f9df08781a836b1fedf408a86d7719de09087925beb70beb1b0245752eaf2aa034b5017119587c2b3') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-macorrplot/lilac.py b/BioArchLinux/r-macorrplot/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-macorrplot/lilac.py +++ b/BioArchLinux/r-macorrplot/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-macorrplot/lilac.yaml b/BioArchLinux/r-macorrplot/lilac.yaml index a4ab24040a..1e2c929f7d 100644 --- a/BioArchLinux/r-macorrplot/lilac.yaml +++ b/BioArchLinux/r-macorrplot/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: maCorrPlot_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/maCorrPlot +- source: rpkgs + pkgname: maCorrPlot + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-mantelcorr/PKGBUILD b/BioArchLinux/r-mantelcorr/PKGBUILD index aefbde7e13..da4c58dc54 100644 --- a/BioArchLinux/r-mantelcorr/PKGBUILD +++ b/BioArchLinux/r-mantelcorr/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=MantelCorr _pkgver=1.72.0 pkgname=r-${_pkgname,,} -pkgver=1.72.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Compute Mantel Cluster Correlations' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Compute Mantel Cluster Correlations" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('408a025f3d22856315b18ec4ddc99fe1fc6dfdfca7bcb8b39c8754cd3778f64b') +md5sums=('7ef5ee0a329a4cf218c340e9289fea32') +b2sums=('3b7455388ae2f355e5334e7a236325310d4088e7ae8f8cee64d30037abc78f190f002fd2341807722e03cf85b52e717ed585d94c9aedc28354f08f54623481f2') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-mantelcorr/lilac.py b/BioArchLinux/r-mantelcorr/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-mantelcorr/lilac.py +++ b/BioArchLinux/r-mantelcorr/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-mantelcorr/lilac.yaml b/BioArchLinux/r-mantelcorr/lilac.yaml index e1d23e4144..8d5c0e0e3a 100644 --- a/BioArchLinux/r-mantelcorr/lilac.yaml +++ b/BioArchLinux/r-mantelcorr/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: MantelCorr_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/MantelCorr +- source: rpkgs + pkgname: MantelCorr + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-marima/PKGBUILD b/BioArchLinux/r-marima/PKGBUILD index 8f1037f257..1015f36e4b 100644 --- a/BioArchLinux/r-marima/PKGBUILD +++ b/BioArchLinux/r-marima/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=marima _pkgver=2.2 pkgname=r-${_pkgname,,} -pkgver=2.2 +pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc='Multivariate ARIMA and ARIMA-X Analysis' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Multivariate ARIMA and ARIMA-X Analysis" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-only') depends=( r ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a6328dfcd3463f80921629e884052901f26740601f4b4f50a4a200924782db0e') +md5sums=('d4ed509e53612f09c04da251444481b1') +b2sums=('6de2b81e045d2e9cfd68051265688e886a01040182440bcd06cf770cbf4a778348324b562249c29108ad9e7a708dbbb5a514d4ed7b5e6215938a0d2dccac1516') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-marima/lilac.py b/BioArchLinux/r-marima/lilac.py index cc91618b28..b5cdb057c5 100644 --- a/BioArchLinux/r-marima/lilac.py +++ b/BioArchLinux/r-marima/lilac.py @@ -1,9 +1,14 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-marima/lilac.yaml b/BioArchLinux/r-marima/lilac.yaml index 685f710519..6d35b44550 100644 --- a/BioArchLinux/r-marima/lilac.yaml +++ b/BioArchLinux/r-marima/lilac.yaml @@ -1,12 +1,10 @@ build_prefix: extra-x86_64 maintainers: - - github: sukanka - email: su975853527@gmail.com -post_build_script: | - git_pkgbuild_commit() - update_aur_repo() +- github: sukanka + email: su975853527@gmail.com update_on: - - regex: marima_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=marima - - alias: r +- source: rpkgs + pkgname: marima + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-massarray/PKGBUILD b/BioArchLinux/r-massarray/PKGBUILD index c49427680c..cc002b2b7b 100644 --- a/BioArchLinux/r-massarray/PKGBUILD +++ b/BioArchLinux/r-massarray/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=MassArray _pkgver=1.54.0 pkgname=r-${_pkgname,,} -pkgver=1.54.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Analytical Tools for MassArray Data' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Analytical Tools for MassArray Data" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('cf223329fed02269a02ba48c62ce3dc34f1968e75b1ff2b149575416770e2bb4') +md5sums=('028fea456ce2e5b3820ad6dc0d1989c1') +b2sums=('8db9948e51b012017d3b3cf0b958eb4e57da4748597bc5c361587c08991d1856089fbf76c62e01327928c003bde4c504d8b538165e4ee14b27ade8c25be4e310') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-massarray/lilac.py b/BioArchLinux/r-massarray/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-massarray/lilac.py +++ b/BioArchLinux/r-massarray/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-massarray/lilac.yaml b/BioArchLinux/r-massarray/lilac.yaml index 0739608394..1afa34dca9 100644 --- a/BioArchLinux/r-massarray/lilac.yaml +++ b/BioArchLinux/r-massarray/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: MassArray_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/MassArray +- source: rpkgs + pkgname: MassArray + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-matchbox/PKGBUILD b/BioArchLinux/r-matchbox/PKGBUILD index 622db925ca..eccc5b46b4 100644 --- a/BioArchLinux/r-matchbox/PKGBUILD +++ b/BioArchLinux/r-matchbox/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=matchBox _pkgver=1.44.0 pkgname=r-${_pkgname,,} -pkgver=1.44.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-2.0') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('3191d06eae4802bcd3e3eab87a15c2ddaae29c46bf1907026cfa8782e86eb1a0') +md5sums=('b6e4b10ee38f433d1bce146a089a44ec') +b2sums=('3d3ea47607e5966961c870ec60a51cd1cedfd401a2ad81f07b5a869363d86e3fc7d358b17a574ea8222fece45d0b8cdcf63486a0979a7ab2f00fb78941019c13') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-matchbox/lilac.py b/BioArchLinux/r-matchbox/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-matchbox/lilac.py +++ b/BioArchLinux/r-matchbox/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-matchbox/lilac.yaml b/BioArchLinux/r-matchbox/lilac.yaml index e29b7d1519..9264f5b935 100644 --- a/BioArchLinux/r-matchbox/lilac.yaml +++ b/BioArchLinux/r-matchbox/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: matchBox_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/matchBox +- source: rpkgs + pkgname: matchBox + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-mbamethyl/PKGBUILD b/BioArchLinux/r-mbamethyl/PKGBUILD index 3653a9a75c..0760aa6f8d 100644 --- a/BioArchLinux/r-mbamethyl/PKGBUILD +++ b/BioArchLinux/r-mbamethyl/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=MBAmethyl _pkgver=1.36.0 pkgname=r-${_pkgname,,} -pkgver=1.36.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Model-based analysis of DNA methylation data' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="Model-based analysis of DNA methylation data" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-2.0') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('87b0b81aec31c0b902ad24e2c2c7f5b281d9afb7f5019459b69be7df36155c08') +md5sums=('0b6ac0d76525c156606d08bcbf606709') +b2sums=('f1880203f354e8aa83147577c8d7f4a89d575ae5cec326704acac8a1df208af46068b1a8b1a64b8243ec00275fe7762c662d567f90fe6e4b9032f4589fbb6f1a') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-mbamethyl/lilac.py b/BioArchLinux/r-mbamethyl/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-mbamethyl/lilac.py +++ b/BioArchLinux/r-mbamethyl/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-mbamethyl/lilac.yaml b/BioArchLinux/r-mbamethyl/lilac.yaml index 3077cbedcd..70c1b2cd1c 100644 --- a/BioArchLinux/r-mbamethyl/lilac.yaml +++ b/BioArchLinux/r-mbamethyl/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: MBAmethyl_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/MBAmethyl +- source: rpkgs + pkgname: MBAmethyl + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-measurementerror.cor/PKGBUILD b/BioArchLinux/r-measurementerror.cor/PKGBUILD index cc3122e296..119fd04be6 100644 --- a/BioArchLinux/r-measurementerror.cor/PKGBUILD +++ b/BioArchLinux/r-measurementerror.cor/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=MeasurementError.cor _pkgver=1.74.0 pkgname=r-${_pkgname,,} -pkgver=1.74.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Measurement Error model estimate for correlation coefficient' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('LGPL') +pkgdesc="Measurement Error model estimate for correlation coefficient" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('LGPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('2e7631fb9bbf651651d983066173f235aa668638ab882f1e983df16b0468ec42') +md5sums=('7de3f5ca3749a7b1e80fdfa66204a252') +b2sums=('afa6d335a3188a6b90cc665031e876e7514e8486d851c84a0806f01fb69c36f44a6bb9543511d352123768353831072d91f976476bd639cd270a7f8181d739b1') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-measurementerror.cor/lilac.py b/BioArchLinux/r-measurementerror.cor/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-measurementerror.cor/lilac.py +++ b/BioArchLinux/r-measurementerror.cor/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + 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('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-measurementerror.cor/lilac.yaml b/BioArchLinux/r-measurementerror.cor/lilac.yaml index 2547d1ec4d..e656977db4 100644 --- a/BioArchLinux/r-measurementerror.cor/lilac.yaml +++ b/BioArchLinux/r-measurementerror.cor/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: MeasurementError.cor_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/MeasurementError.cor +- source: rpkgs + pkgname: MeasurementError.cor + repo: bioc + md5: true - alias: r