diff --git a/BioArchLinux/r-somnibus/PKGBUILD b/BioArchLinux/r-somnibus/PKGBUILD index 53620d5d56..60e059741d 100644 --- a/BioArchLinux/r-somnibus/PKGBUILD +++ b/BioArchLinux/r-somnibus/PKGBUILD @@ -1,16 +1,16 @@ -# Maintainer: Guoyi Zhang +# Maintainer: Pekka Ristola +# Contributor: Guoyi Zhang _pkgname=SOMNiBUS -_pkgver=1.7.0 +_pkgver=1.10.0 pkgname=r-${_pkgname,,} -pkgver=1.7.0 -pkgrel=2 -pkgdesc='Smooth modeling of bisulfite sequencing' -arch=('any') +pkgver=${_pkgver//-/.} +pkgrel=0 +pkgdesc="Smooth modeling of bisulfite sequencing" +arch=(any) url="https://bioconductor.org/packages/${_pkgname}" -license=('MIT') +license=(MIT) depends=( - r r-annotatr r-biocmanager r-bsseq @@ -40,15 +40,18 @@ optdepends=( r-txdb.hsapiens.ucsc.hg38.knowngene ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('1baf115a020f2ae781493ec36f0696a72c24ee8e5aaeb0ce7a01609881abaaa5') +md5sums=('0865c015122f915127302bf751a10812') +sha256sums=('4f464b57f1b26664210e3b43072969ec4eb77f6f1c7b0b15149692994318ba89') 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}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_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-somnibus/lilac.py b/BioArchLinux/r-somnibus/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-somnibus/lilac.py +++ b/BioArchLinux/r-somnibus/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-somnibus/lilac.yaml b/BioArchLinux/r-somnibus/lilac.yaml index c7934c2825..c87695ec02 100644 --- a/BioArchLinux/r-somnibus/lilac.yaml +++ b/BioArchLinux/r-somnibus/lilac.yaml @@ -1,7 +1,7 @@ build_prefix: extra-x86_64 maintainers: -- github: starsareintherose - email: kuoi@bioarchlinux.org +- github: pekkarr + email: pekkarr@protonmail.com repo_depends: - r-annotatr - r-biocmanager @@ -18,7 +18,8 @@ repo_depends: - r-vgam - r-yaml update_on: -- regex: SOMNiBUS_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/SOMNiBUS +- source: rpkgs + pkgname: SOMNiBUS + repo: bioc + md5: true - alias: r