diff --git a/BioArchLinux/r-flowpeaks/PKGBUILD b/BioArchLinux/r-flowpeaks/PKGBUILD index 7741f42337..df7d6db69d 100644 --- a/BioArchLinux/r-flowpeaks/PKGBUILD +++ b/BioArchLinux/r-flowpeaks/PKGBUILD @@ -1,31 +1,28 @@ -# system requirements: gsl # Maintainer: Guoyi Zhang _pkgname=flowPeaks _pkgver=1.48.0 pkgname=r-${_pkgname,,} -pkgver=1.48.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='An R package for flow data clustering' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="An R package for flow data clustering" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-1.0-Perl') depends=( - r gsl -) -optdepends=( - r-flowcore + r ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('84baaf3c7e8c2cd9790dfd086bf56ce07d448be6255285330dfc92b0b2fafafb') +md5sums=('f68db373a0d053a7eabd112df80a25f1') +b2sums=('b1e0e5cea694f73ce830aa3e7f166f5dc17b2d5d2bf1cabb6a7ce6daf91884bdf087c1c998ab8dac340feee8471ed06df1eb14e793ef2d0923f3be33ea49a18c') 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-flowpeaks/lilac.py b/BioArchLinux/r-flowpeaks/lilac.py index bd219c037c..962c1669ea 100644 --- a/BioArchLinux/r-flowpeaks/lilac.py +++ b/BioArchLinux/r-flowpeaks/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 = "gsl", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-flowpeaks/lilac.yaml b/BioArchLinux/r-flowpeaks/lilac.yaml index 646d7ac60c..7795ac876d 100644 --- a/BioArchLinux/r-flowpeaks/lilac.yaml +++ b/BioArchLinux/r-flowpeaks/lilac.yaml @@ -3,7 +3,12 @@ maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org update_on: -- regex: flowPeaks_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/flowPeaks +- source: rpkgs + pkgname: flowPeaks + repo: bioc + md5: true - alias: r +- source: alpmfiles + pkgname: gsl + filename: usr/lib/libgsl\.so\.([^.]+) + repo: extra diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py index c131810611..aa06600635 100644 --- a/lilac-extensions/lilac_r_utils.py +++ b/lilac-extensions/lilac_r_utils.py @@ -191,6 +191,7 @@ license_map = { "Apache License (>= 2)": "Apache", "Apache License (>= 2.0)": "Apache", "Apache License 2.0": "Apache", + "Artistic-1.0": "Artistic-1.0-Perl", "Artistic-2.0": "Artistic2.0", "BSD_2_clause + file LICENSE": "BSD", "BSD_3_clause + file LICENSE": "BSD",