From 6293732ce6f37ddaed00eb7ba28a1dc853781738 Mon Sep 17 00:00:00 2001 From: Pekka Ristola Date: Sat, 9 Mar 2024 13:44:50 +0200 Subject: [PATCH] r-*: use metadata checks for several packages --- BioArchLinux/r-clipr/PKGBUILD | 26 +++++++++++++----------- BioArchLinux/r-clipr/lilac.py | 14 ++++++++----- BioArchLinux/r-clipr/lilac.yaml | 7 ++++--- BioArchLinux/r-exactranktests/PKGBUILD | 24 ++++++++++------------ BioArchLinux/r-exactranktests/lilac.py | 11 +++++----- BioArchLinux/r-exactranktests/lilac.yaml | 7 ++++--- BioArchLinux/r-geem/PKGBUILD | 21 ++++++++++--------- BioArchLinux/r-geem/lilac.py | 11 +++++----- BioArchLinux/r-geem/lilac.yaml | 7 ++++--- BioArchLinux/r-ismev/PKGBUILD | 21 ++++++++++--------- BioArchLinux/r-ismev/lilac.py | 11 +++++----- BioArchLinux/r-ismev/lilac.yaml | 7 ++++--- BioArchLinux/r-log4r/PKGBUILD | 19 +++++++++-------- BioArchLinux/r-log4r/lilac.py | 11 +++++----- BioArchLinux/r-log4r/lilac.yaml | 7 ++++--- BioArchLinux/r-mcmc/PKGBUILD | 23 ++++++++++++--------- BioArchLinux/r-mcmc/lilac.py | 11 +++++----- BioArchLinux/r-mcmc/lilac.yaml | 7 ++++--- BioArchLinux/r-mircompdata/PKGBUILD | 21 ++++++++++--------- BioArchLinux/r-mircompdata/lilac.py | 14 ++++++++----- BioArchLinux/r-mircompdata/lilac.yaml | 7 ++++--- BioArchLinux/r-smvar/PKGBUILD | 21 ++++++++++--------- BioArchLinux/r-smvar/lilac.py | 11 +++++----- BioArchLinux/r-smvar/lilac.yaml | 7 ++++--- BioArchLinux/r-stabs/PKGBUILD | 21 ++++++++++--------- BioArchLinux/r-stabs/lilac.py | 11 +++++----- BioArchLinux/r-stabs/lilac.yaml | 7 ++++--- 27 files changed, 199 insertions(+), 166 deletions(-) diff --git a/BioArchLinux/r-clipr/PKGBUILD b/BioArchLinux/r-clipr/PKGBUILD index 906344152a..44337cdf83 100644 --- a/BioArchLinux/r-clipr/PKGBUILD +++ b/BioArchLinux/r-clipr/PKGBUILD @@ -1,20 +1,21 @@ -# system requirements: xclip (https://github.com/astrand/xclip) or xsel(http://www.vergenet.net/~conrad/software/xsel/) for accessingthe X11 clipboard # Maintainer: Guoyi Zhang _pkgname=clipr _pkgver=0.8.0 pkgname=r-${_pkgname,,} -pkgver=0.8.0 +pkgver=${_pkgver//-/.} pkgrel=8 -pkgdesc='Read and Write from the System Clipboard' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Read and Write from the System Clipboard" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-only') depends=( r - xclip ) optdepends=( + "wl-clipboard: accessing Wayland clipboard" + "xclip: accessing X11 clipboard" + "xsel: alternative for accessing X11 clipboard" r-covr r-knitr r-rmarkdown @@ -22,14 +23,15 @@ optdepends=( r-testthat ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9') +md5sums=('558ddf145114bbc0272e6aed05b8e5fe') +b2sums=('6b489ff1b8353942a327a550eaf9f1f693d74809515990b4e9dc666d7829532d89f368aeb081413dfb7a1e4aeedbb247c570f3187310078ea8bbf264d9b0bb2d') 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-clipr/lilac.py b/BioArchLinux/r-clipr/lilac.py index 620556bc87..fec189d6c3 100644 --- a/BioArchLinux/r-clipr/lilac.py +++ b/BioArchLinux/r-clipr/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_systemrequirements = "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-clipr/lilac.yaml b/BioArchLinux/r-clipr/lilac.yaml index a1d3b5a45e..89a6ebad5e 100644 --- a/BioArchLinux/r-clipr/lilac.yaml +++ b/BioArchLinux/r-clipr/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: clipr_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=clipr +- source: rpkgs + pkgname: clipr + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-exactranktests/PKGBUILD b/BioArchLinux/r-exactranktests/PKGBUILD index 1464e214f5..507ef1b70b 100644 --- a/BioArchLinux/r-exactranktests/PKGBUILD +++ b/BioArchLinux/r-exactranktests/PKGBUILD @@ -3,27 +3,25 @@ _pkgname=exactRankTests _pkgver=0.8-35 pkgname=r-${_pkgname,,} -pkgver=0.8.35 +pkgver=${_pkgver//-/.} pkgrel=5 -pkgdesc='Exact Distributions for Rank and Permutation Tests' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Exact Distributions for Rank and Permutation Tests" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) -optdepends=( - r-survival -) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('7eb4a9ff431a306f634a5feba39c381afb17573e24230976ece843c84e8969e3') +md5sums=('5c3767db5ff0c9d69b9990d4443f0cad') +b2sums=('513d696cc55e2663ee8f722bc441c5ec5b0f7f9438ccaacd255e09bf40b93315cd6dd33054a433fbd7a3b29a01bac22a252dc956e57522c443763ba71f31c9a7') 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-exactranktests/lilac.py b/BioArchLinux/r-exactranktests/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-exactranktests/lilac.py +++ b/BioArchLinux/r-exactranktests/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-exactranktests/lilac.yaml b/BioArchLinux/r-exactranktests/lilac.yaml index 34e5f268eb..7edc11e256 100644 --- a/BioArchLinux/r-exactranktests/lilac.yaml +++ b/BioArchLinux/r-exactranktests/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: exactRankTests_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=exactRankTests +- source: rpkgs + pkgname: exactRankTests + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-geem/PKGBUILD b/BioArchLinux/r-geem/PKGBUILD index 55daf97dc6..982ba62a0e 100644 --- a/BioArchLinux/r-geem/PKGBUILD +++ b/BioArchLinux/r-geem/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=geeM _pkgver=0.10.1 pkgname=r-${_pkgname,,} -pkgver=0.10.1 +pkgver=${_pkgver//-/.} pkgrel=8 -pkgdesc='Solve Generalized Estimating Equations' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Solve Generalized Estimating Equations" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-only') depends=( r ) @@ -18,14 +18,15 @@ optdepends=( r-testthat ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5') +md5sums=('e493043dac3bd7c57b104ace2a6e19d7') +b2sums=('584fc4ee474abf2c53b7aa6b6a0f602c636eac3fa9d9b87e797aaa69c1d905b535eb8094e6e91608968a4d0227d5249650c17c4e41cecd80957829dfdd52180d') 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-geem/lilac.py b/BioArchLinux/r-geem/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-geem/lilac.py +++ b/BioArchLinux/r-geem/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-geem/lilac.yaml b/BioArchLinux/r-geem/lilac.yaml index ce878bdd33..763ad0168d 100644 --- a/BioArchLinux/r-geem/lilac.yaml +++ b/BioArchLinux/r-geem/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: geeM_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=geeM +- source: rpkgs + pkgname: geeM + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-ismev/PKGBUILD b/BioArchLinux/r-ismev/PKGBUILD index 92e5043041..a75264f4f6 100644 --- a/BioArchLinux/r-ismev/PKGBUILD +++ b/BioArchLinux/r-ismev/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=ismev _pkgver=1.42 pkgname=r-${_pkgname,,} -pkgver=1.42 +pkgver=${_pkgver//-/.} pkgrel=6 -pkgdesc='An Introduction to Statistical Modeling of Extreme Values' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="An Introduction to Statistical Modeling of Extreme Values" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('0d57fbeca83bd478e84fcff795967d51d8448c629abe7adc6c4c18c7fb8bf1a5') +md5sums=('35d6f5fa7f29eb822d4efad81b3dd59e') +b2sums=('c87b907c13e55c16ecf71180fd66cf16ebce1cf225efa9139e30fa4953f275a18d8c33d02b5413cfc68ac1ef2ed8e9d09a29d5c81a60fc1989660a80cbb913f3') 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-ismev/lilac.py b/BioArchLinux/r-ismev/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-ismev/lilac.py +++ b/BioArchLinux/r-ismev/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-ismev/lilac.yaml b/BioArchLinux/r-ismev/lilac.yaml index ad344859e1..2e6c4cdbf5 100644 --- a/BioArchLinux/r-ismev/lilac.yaml +++ b/BioArchLinux/r-ismev/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: ismev_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=ismev +- source: rpkgs + pkgname: ismev + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-log4r/PKGBUILD b/BioArchLinux/r-log4r/PKGBUILD index 158f1cfa56..0ce95e6b62 100644 --- a/BioArchLinux/r-log4r/PKGBUILD +++ b/BioArchLinux/r-log4r/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=log4r _pkgver=0.4.3 pkgname=r-${_pkgname,,} -pkgver=0.4.3 +pkgver=${_pkgver//-/.} pkgrel=2 pkgdesc="A Fast and Lightweight Logging System for R, Based on 'log4j'" -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('Artistic2.0') +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('Artistic-2.0') depends=( r ) @@ -28,14 +28,15 @@ optdepends=( r-testthat ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('dfe3d49d35a8d8f3ad63f156d18e860540a01bd0af0e343cbab3e31a2cf5904c') +md5sums=('48d5f4212c65e91cbd900c2fbaf2f3d6') +b2sums=('2ba50dbe1312f564dba282afda0adf9ecbd1b7f4e2e7e9ddb2b1f12f398286c5523321d7686c0733831d19b0d05024f485f90d93b59cd721570c94a8891ee31e') 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-log4r/lilac.py b/BioArchLinux/r-log4r/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-log4r/lilac.py +++ b/BioArchLinux/r-log4r/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-log4r/lilac.yaml b/BioArchLinux/r-log4r/lilac.yaml index 032917e82b..f69c488147 100644 --- a/BioArchLinux/r-log4r/lilac.yaml +++ b/BioArchLinux/r-log4r/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: log4r_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=log4r +- source: rpkgs + pkgname: log4r + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-mcmc/PKGBUILD b/BioArchLinux/r-mcmc/PKGBUILD index 2692cb4d47..a423d150a8 100644 --- a/BioArchLinux/r-mcmc/PKGBUILD +++ b/BioArchLinux/r-mcmc/PKGBUILD @@ -3,11 +3,11 @@ _pkgname=mcmc _pkgver=0.9-8 pkgname=r-${_pkgname,,} -pkgver=0.9.8 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Markov Chain Monte Carlo' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" +pkgdesc="Markov Chain Monte Carlo" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" license=('MIT') depends=( r @@ -17,15 +17,18 @@ optdepends=( r-xtable ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7') +md5sums=('429599a7f24105629c41dd7c9f36b992') +b2sums=('d804249a6244e3104687497c83472ec69411e05f3ce580d11b79b3a0278ed2c27d8b902ca6aa3d87f8da3ec169249ffb135ac99e4db17dc688e144e6b95912d7') 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-mcmc/lilac.py b/BioArchLinux/r-mcmc/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-mcmc/lilac.py +++ b/BioArchLinux/r-mcmc/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-mcmc/lilac.yaml b/BioArchLinux/r-mcmc/lilac.yaml index 37a786ad07..786e20b4fb 100644 --- a/BioArchLinux/r-mcmc/lilac.yaml +++ b/BioArchLinux/r-mcmc/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: mcmc_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=mcmc +- source: rpkgs + pkgname: mcmc + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-mircompdata/PKGBUILD b/BioArchLinux/r-mircompdata/PKGBUILD index 753ea938d0..4ad457ac27 100644 --- a/BioArchLinux/r-mircompdata/PKGBUILD +++ b/BioArchLinux/r-mircompdata/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=miRcompData _pkgver=1.32.0 pkgname=r-${_pkgname,,} -pkgver=1.32.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Data used in the miRcomp package' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Data used in the miRcomp package" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( r ) source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('e61d11cd0352745d221517f0f85654ad6e5923d2670eeff0069797db1bdd8897') +md5sums=('0b091222ebe8ac1a3a2c59384931393b') +b2sums=('1c41da4e325c58fd0d510c945e2c7fdb76d760557b79890ec5ffc5a967b4993b2a66b3b4f270314ee9848acc288a585ef2b87d1150dbc0c08a8c82a975bbb911') 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-mircompdata/lilac.py b/BioArchLinux/r-mircompdata/lilac.py index bd219c037c..b5d481821a 100644 --- a/BioArchLinux/r-mircompdata/lilac.py +++ b/BioArchLinux/r-mircompdata/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 = "GPL-3 | file LICENSE", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-mircompdata/lilac.yaml b/BioArchLinux/r-mircompdata/lilac.yaml index 91dc7edd2c..9d861ae294 100644 --- a/BioArchLinux/r-mircompdata/lilac.yaml +++ b/BioArchLinux/r-mircompdata/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: miRcompData_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/miRcompData +- source: rpkgs + pkgname: miRcompData + repo: bioc-data-experiment + md5: true - alias: r diff --git a/BioArchLinux/r-smvar/PKGBUILD b/BioArchLinux/r-smvar/PKGBUILD index 708989f2b8..64db57d8f4 100644 --- a/BioArchLinux/r-smvar/PKGBUILD +++ b/BioArchLinux/r-smvar/PKGBUILD @@ -3,24 +3,25 @@ _pkgname=SMVar _pkgver=1.3.4 pkgname=r-${_pkgname,,} -pkgver=1.3.4 +pkgver=${_pkgver//-/.} pkgrel=7 -pkgdesc='Structural Model for variances' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Structural Model for Variances" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( r ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('aaea3ef7da6cee1bb86fef166df766229c8b7cac9fcf5bc28da7adff5e2c01d6') +md5sums=('0cad7d2abfd4be6306eaf2bce923ce7d') +b2sums=('da5e76b6e6ecd9d2992943429056ee6956509e9414e15a537e640ecff7efe190029e5c6f726138fb325fac1ffec4fe1fc1d2c54f647d55fcedbacae4f46b912b') 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-smvar/lilac.py b/BioArchLinux/r-smvar/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-smvar/lilac.py +++ b/BioArchLinux/r-smvar/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-smvar/lilac.yaml b/BioArchLinux/r-smvar/lilac.yaml index 642fd109a6..5083cd46e0 100644 --- a/BioArchLinux/r-smvar/lilac.yaml +++ b/BioArchLinux/r-smvar/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: SMVar_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=SMVar +- source: rpkgs + pkgname: SMVar + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-stabs/PKGBUILD b/BioArchLinux/r-stabs/PKGBUILD index 7d7610e7eb..0f6e0f964e 100644 --- a/BioArchLinux/r-stabs/PKGBUILD +++ b/BioArchLinux/r-stabs/PKGBUILD @@ -3,12 +3,12 @@ _pkgname=stabs _pkgver=0.6-4 pkgname=r-${_pkgname,,} -pkgver=0.6.4 +pkgver=${_pkgver//-/.} pkgrel=8 -pkgdesc='Stability Selection with Error Control' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Stability Selection with Error Control" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-only') depends=( r ) @@ -24,14 +24,15 @@ optdepends=( r-th.data ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('f8507337789f668e421a6ee7b11dd5ea331bf8bff0f9702dd1b93f46c2f3c1d9') +md5sums=('b05e82dca362b6442b1c2d2970252509') +b2sums=('4c29ed288d3386fe6293b9eeb11fb316879ecb6a1d1198e8fab711fd9b60f283072ea1c0b040d0cd67aa7d34222979a480ae13170b905855e0b72287e9f80108') 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-stabs/lilac.py b/BioArchLinux/r-stabs/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-stabs/lilac.py +++ b/BioArchLinux/r-stabs/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-stabs/lilac.yaml b/BioArchLinux/r-stabs/lilac.yaml index 65007dea0f..d9147def6c 100644 --- a/BioArchLinux/r-stabs/lilac.yaml +++ b/BioArchLinux/r-stabs/lilac.yaml @@ -3,7 +3,8 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: stabs_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=stabs +- source: rpkgs + pkgname: stabs + repo: cran + md5: true - alias: r