diff --git a/BioArchLinux/r-limma/PKGBUILD b/BioArchLinux/r-limma/PKGBUILD index 3f593de862..341bb1eb4f 100644 --- a/BioArchLinux/r-limma/PKGBUILD +++ b/BioArchLinux/r-limma/PKGBUILD @@ -1,42 +1,43 @@ -# Maintainer: Guoyi Zhang +# Maintainer: Pekka Ristola +# Contributor: Guoyi Zhang _pkgname=limma -_pkgver=3.56.2 +_pkgver=3.58.0 pkgname=r-${_pkgname,,} -pkgver=3.56.2 -pkgrel=1 -pkgdesc='Linear Models for Microarray Data' -arch=('x86_64') +pkgver=${_pkgver//-/.} +pkgrel=0 +pkgdesc="Linear Models for Microarray Data" +arch=(x86_64) url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +license=(GPL) depends=( - r + r-statmod ) optdepends=( r-affy r-annotationdbi r-biasedurn r-biobase + r-biocstyle r-ellipse r-go.db r-gplots r-illuminaio + r-knitr r-locfit - r-mass r-org.hs.eg.db - r-splines - r-statmod r-vsn ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('19d8090708a38d7320e797df27455e60eaafdc02f97ecae62537d8ec925a3e56') +md5sums=('521e5f19c19affa0ead9e097967701e8') +sha256sums=('ee4510e8208e564dc5d32c2ba58741b6a3c155e9b90c5fe4a299e98886f71fd6') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir -p build + R CMD INSTALL "$_pkgname" -l build } 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-limma/lilac.py b/BioArchLinux/r-limma/lilac.py index bd219c037c..2dfb55e88c 100644 --- a/BioArchLinux/r-limma/lilac.py +++ b/BioArchLinux/r-limma/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 (>=2)", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-limma/lilac.yaml b/BioArchLinux/r-limma/lilac.yaml index 8af1c727e6..0c32d0a578 100644 --- a/BioArchLinux/r-limma/lilac.yaml +++ b/BioArchLinux/r-limma/lilac.yaml @@ -1,9 +1,12 @@ build_prefix: extra-x86_64 maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-statmod update_on: -- regex: limma_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/limma +- source: rpkgs + pkgname: limma + repo: bioc + md5: true - alias: r