diff --git a/BioArchLinux/r-enmix/PKGBUILD b/BioArchLinux/r-enmix/PKGBUILD index 0ce09dec76..fed4ed05f7 100644 --- a/BioArchLinux/r-enmix/PKGBUILD +++ b/BioArchLinux/r-enmix/PKGBUILD @@ -1,16 +1,16 @@ -# Maintainer: Guoyi Zhang +# Maintainer: Pekka Ristola +# Contributor: Guoyi Zhang _pkgname=ENmix -_pkgver=1.36.03 +_pkgver=1.36.05 pkgname=r-${_pkgname,,} -pkgver=1.36.03 -pkgrel=1 -pkgdesc='Quality control and analysis tools for Illumina DNA methylation BeadChip' -arch=('any') +pkgver=${_pkgver//-/.} +pkgrel=0 +pkgdesc="Quality control and analysis tools for Illumina DNA methylation BeadChip" +arch=(any) url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +license=(Artistic2.0) depends=( - r r-annotationhub r-biobase r-doparallel @@ -24,14 +24,19 @@ depends=( r-illuminaio r-impute r-iranges + r-irlba r-matrixstats r-minfi - r-preprocesscore r-quadprog r-rpmm r-s4vectors r-summarizedexperiment ) +checkdepends=( + r-biocgenerics + r-minfidata + r-runit +) optdepends=( r-biocgenerics r-biocstyle @@ -41,14 +46,20 @@ optdepends=( r-runit ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('fd1d9494c9e829b8515606985b0b6da7662a0cd0427e33c42c9fa6e427e044ce') +md5sums=('54dd30838866aa7f27b2a93430483f58') +sha256sums=('dd6c80b26ffe7104b392d41e5f33c2ee758b440ed23267543f852c30f69cd936') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" Rscript --vanilla runTests.R } 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-enmix/lilac.py b/BioArchLinux/r-enmix/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-enmix/lilac.py +++ b/BioArchLinux/r-enmix/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-enmix/lilac.yaml b/BioArchLinux/r-enmix/lilac.yaml index 3c06ab937d..59ea50bb3b 100644 --- a/BioArchLinux/r-enmix/lilac.yaml +++ b/BioArchLinux/r-enmix/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-annotationhub - r-biobase @@ -16,15 +16,20 @@ repo_depends: - r-illuminaio - r-impute - r-iranges +- r-irlba - r-matrixstats - r-minfi -- r-preprocesscore - r-quadprog - r-rpmm - r-s4vectors - r-summarizedexperiment +repo_makedepends: +- r-biocgenerics +- r-minfidata +- r-runit update_on: -- regex: ENmix_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/ENmix +- source: rpkgs + pkgname: ENmix + repo: bioc + md5: true - alias: r