diff --git a/BioArchLinux/r-flowplots/PKGBUILD b/BioArchLinux/r-flowplots/PKGBUILD index 5e7dfbaaf6..3e8e6389c0 100644 --- a/BioArchLinux/r-flowplots/PKGBUILD +++ b/BioArchLinux/r-flowplots/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=flowPlots _pkgver=1.50.0 pkgname=r-${_pkgname,,} -pkgver=1.50.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='flowPlots: analysis plots and data class for gated flow cytometry data' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="analysis plots and data class for gated flow cytometry data" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-2.0') depends=( r ) @@ -16,14 +16,15 @@ optdepends=( r-vcd ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('9ac84c0a3af3071a4dd2dbc70883105eced78c1996f1f282002dd0ccea7cb8d1') +md5sums=('523b0d79646813f56d711d3e0f38a5e9') +b2sums=('5b35b308070ff5bef1d1dd8ade1633843eb34202f32dcc311fe8519b28184e4d940446bec0f71d898d13acdc70a9899338f3d10753f62aeee544ede5ca309b92') 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-flowplots/lilac.py b/BioArchLinux/r-flowplots/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-flowplots/lilac.py +++ b/BioArchLinux/r-flowplots/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-flowplots/lilac.yaml b/BioArchLinux/r-flowplots/lilac.yaml index c617888e73..d064823af1 100644 --- a/BioArchLinux/r-flowplots/lilac.yaml +++ b/BioArchLinux/r-flowplots/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: flowPlots_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/flowPlots +- source: rpkgs + pkgname: flowPlots + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-fmrs/PKGBUILD b/BioArchLinux/r-fmrs/PKGBUILD index 2de4955c95..65c73cd239 100644 --- a/BioArchLinux/r-fmrs/PKGBUILD +++ b/BioArchLinux/r-fmrs/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=fmrs _pkgver=1.12.0 pkgname=r-${_pkgname,,} -pkgver=1.12.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Variable Selection in Finite Mixture of AFT Regression and FMR' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Variable Selection in Finite Mixture of AFT Regression and FMR Models" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( r ) @@ -16,17 +16,17 @@ optdepends=( r-biocgenerics r-knitr r-testthat - r-utils ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('6a9566cda423e834136eed456b6f702de7ed37c7624b06656d60417b793e57e3') +md5sums=('ccf41504ab27d93464e555b363ef406a') +b2sums=('f8b92bfe2b48cf70c50532ab837b13924006632d4265f4382ccc4609bcd9ea2fc0495fe4a2bb42a124482ed867444684272b235533bf2c367c6703b93854f0ca') 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-fmrs/lilac.py b/BioArchLinux/r-fmrs/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-fmrs/lilac.py +++ b/BioArchLinux/r-fmrs/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-fmrs/lilac.yaml b/BioArchLinux/r-fmrs/lilac.yaml index dec3323eb1..ee52405f8b 100644 --- a/BioArchLinux/r-fmrs/lilac.yaml +++ b/BioArchLinux/r-fmrs/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: fmrs_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/fmrs +- source: rpkgs + pkgname: fmrs + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-garfield/PKGBUILD b/BioArchLinux/r-garfield/PKGBUILD index d46749d87e..4ddf42401b 100644 --- a/BioArchLinux/r-garfield/PKGBUILD +++ b/BioArchLinux/r-garfield/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=garfield _pkgver=1.30.0 pkgname=r-${_pkgname,,} -pkgver=1.30.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( r ) @@ -16,14 +16,15 @@ optdepends=( r-knitr ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('5841ed36941fad56a90d254a6396301432014af124144593d88e0efd72008a06') +md5sums=('bf1974925a6c10b95ada01ff6d46bf15') +b2sums=('df24e1ee2360e81ee2ac1b7f4a8a32e9dfa14610575d4dbc85831859960ceaa796c0c7b9cceed05ea933411aadd31ac8ef8af77f4809a9970ee9ed39bf40c467') 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-garfield/lilac.py b/BioArchLinux/r-garfield/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-garfield/lilac.py +++ b/BioArchLinux/r-garfield/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-garfield/lilac.yaml b/BioArchLinux/r-garfield/lilac.yaml index b742c05f39..68c8773021 100644 --- a/BioArchLinux/r-garfield/lilac.yaml +++ b/BioArchLinux/r-garfield/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: garfield_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/garfield +- source: rpkgs + pkgname: garfield + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-gbrd/PKGBUILD b/BioArchLinux/r-gbrd/PKGBUILD index a6d3430041..a153d89ffe 100644 --- a/BioArchLinux/r-gbrd/PKGBUILD +++ b/BioArchLinux/r-gbrd/PKGBUILD @@ -4,24 +4,25 @@ _pkgname=gbRd _pkgver=0.4-11 pkgname=r-${_pkgname,,} -pkgver=0.4.11 +pkgver=${_pkgver//-/.} pkgrel=3 -pkgdesc='Utilities for processing Rd objects and files' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Utilities for processing Rd objects and files" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b') +md5sums=('7d43d8e79f3cbdc917f44817a34d2d37') +b2sums=('a7a68f4c58848057567252e2b437016a17bb95d98449b7268a5327d9c40d88863572342add28735599965308e7bba25d3c1e7be8b06c3283e6402ccec3082665') 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-gbrd/lilac.py b/BioArchLinux/r-gbrd/lilac.py index bd219c037c..dc94522131 100644 --- a/BioArchLinux/r-gbrd/lilac.py +++ b/BioArchLinux/r-gbrd/lilac.py @@ -1,12 +1,16 @@ #!/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, + expect_needscompilation = "", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-gbrd/lilac.yaml b/BioArchLinux/r-gbrd/lilac.yaml index bb1c15cdb4..a7403bdd13 100644 --- a/BioArchLinux/r-gbrd/lilac.yaml +++ b/BioArchLinux/r-gbrd/lilac.yaml @@ -1,9 +1,10 @@ build_prefix: extra-x86_64 maintainers: - - github: sukanka - email: su975853527@gmail.com +- github: sukanka + email: su975853527@gmail.com update_on: - - regex: gbRd_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=gbRd - - alias: r +- source: rpkgs + pkgname: gbRd + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-genocn/PKGBUILD b/BioArchLinux/r-genocn/PKGBUILD index 7a51987f11..00c08497f5 100644 --- a/BioArchLinux/r-genocn/PKGBUILD +++ b/BioArchLinux/r-genocn/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=genoCN _pkgver=1.54.0 pkgname=r-${_pkgname,,} -pkgver=1.54.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='genotyping and copy number study tools' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="genotyping and copy number study tools" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('f3ddee592b99af2e2fb9b564e58930f117e5dbbe5a794dc6eee6ecdaf8519f88') +md5sums=('ebc7fc5cb3b5c2bcd98718a7bcd95d6a') +b2sums=('f1ba4cf2c955c7ae94a4bca074110f396a08e2dc1e42fe534266d76848a5c2528ab434b0147c3f0406d5fb708dca1df0603c67709153b9854643bd26806df7c2') 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-genocn/lilac.py b/BioArchLinux/r-genocn/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-genocn/lilac.py +++ b/BioArchLinux/r-genocn/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-genocn/lilac.yaml b/BioArchLinux/r-genocn/lilac.yaml index f5a6fec157..88e41e355b 100644 --- a/BioArchLinux/r-genocn/lilac.yaml +++ b/BioArchLinux/r-genocn/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: genoCN_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/genoCN +- source: rpkgs + pkgname: genoCN + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-globalseq/PKGBUILD b/BioArchLinux/r-globalseq/PKGBUILD index 14a4e0e98a..3be88f0d04 100644 --- a/BioArchLinux/r-globalseq/PKGBUILD +++ b/BioArchLinux/r-globalseq/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=globalSeq _pkgver=1.30.0 pkgname=r-${_pkgname,,} -pkgver=1.30.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Global Test for Counts' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Global Test for Counts" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( r ) @@ -19,14 +19,15 @@ optdepends=( r-testthat ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('e71a151ac910673542fbb47fd6c453cc00c6f21630fde9cf645ba39a399318ac') +md5sums=('1b427214cf1345b8d75ba69dc02adb77') +b2sums=('aa04d988e6f966e02ab983eb008bf26df43741297f2d01159aabf9dd2b28fde158d6c41c71f7904fb85573e65a02db7b87930f40ef104fa533cf623991f5feb9') 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-globalseq/lilac.py b/BioArchLinux/r-globalseq/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-globalseq/lilac.py +++ b/BioArchLinux/r-globalseq/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-globalseq/lilac.yaml b/BioArchLinux/r-globalseq/lilac.yaml index 22d610f2ab..ea056f5768 100644 --- a/BioArchLinux/r-globalseq/lilac.yaml +++ b/BioArchLinux/r-globalseq/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: globalSeq_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/globalSeq +- source: rpkgs + pkgname: globalSeq + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-gpls/PKGBUILD b/BioArchLinux/r-gpls/PKGBUILD index 54c23fe6cb..5d317ce53f 100644 --- a/BioArchLinux/r-gpls/PKGBUILD +++ b/BioArchLinux/r-gpls/PKGBUILD @@ -3,27 +3,25 @@ _pkgname=gpls _pkgver=1.74.0 pkgname=r-${_pkgname,,} -pkgver=1.74.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Classification using generalized partial least squares' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="Classification using generalized partial least squares" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-2.0') depends=( r ) -optdepends=( - r-mass -) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('406afeee1ab2ebcc3a5ec952acf0143e558d130668a48e36147e612e196ed5fc') +md5sums=('db6bc720156a5f7571a34e64b1189d3b') +b2sums=('f647d89a455f050a3189a23cca82b14697f1ea5aebd6851900353cee91747f52f66f4d97550fa0d8c14a57fd97993ed8fadd11110aaf108cfd91e8d7a2ba61ca') 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-gpls/lilac.py b/BioArchLinux/r-gpls/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-gpls/lilac.py +++ b/BioArchLinux/r-gpls/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-gpls/lilac.yaml b/BioArchLinux/r-gpls/lilac.yaml index 201e7c9791..f0a2885347 100644 --- a/BioArchLinux/r-gpls/lilac.yaml +++ b/BioArchLinux/r-gpls/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: gpls_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/gpls +- source: rpkgs + pkgname: gpls + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-graphalignment/PKGBUILD b/BioArchLinux/r-graphalignment/PKGBUILD index 753c2cbd79..13e440c19d 100644 --- a/BioArchLinux/r-graphalignment/PKGBUILD +++ b/BioArchLinux/r-graphalignment/PKGBUILD @@ -3,25 +3,28 @@ _pkgname=GraphAlignment _pkgver=1.66.0 pkgname=r-${_pkgname,,} -pkgver=1.66.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='GraphAlignment' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('custom') +pkgdesc="GraphAlignment" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('LicenseRef-GraphAlignment') depends=( r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('1a446d803266504325225dab0657932018e94c954fd2121769abd4baed90513e') +md5sums=('0bc71a4722d0771d97671e81103bc8bb') +b2sums=('e0a493bc0ef7423360c0dd3c9566666adbfcdb61410db2abb4fc34bc6582f0c651a7eefd58acf15d252fc15316534bba05d725b29587704eacdf37dea7ef8880') 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}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" + + install -d "$pkgdir/usr/share/licenses/$pkgname" + ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-graphalignment/lilac.py b/BioArchLinux/r-graphalignment/lilac.py index bd219c037c..c808eaf563 100644 --- a/BioArchLinux/r-graphalignment/lilac.py +++ b/BioArchLinux/r-graphalignment/lilac.py @@ -1,12 +1,16 @@ #!/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, + expect_license = "file LICENSE", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-graphalignment/lilac.yaml b/BioArchLinux/r-graphalignment/lilac.yaml index 1dbd59153b..a679ac9d6d 100644 --- a/BioArchLinux/r-graphalignment/lilac.yaml +++ b/BioArchLinux/r-graphalignment/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: GraphAlignment_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/GraphAlignment +- source: rpkgs + pkgname: GraphAlignment + repo: bioc + md5: true - alias: r