diff options
Diffstat (limited to 'PKGBUILD')
-rw-r--r-- | PKGBUILD | 45 |
1 files changed, 29 insertions, 16 deletions
@@ -1,19 +1,16 @@ -# system requirements: C++11 -# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net> +# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com> +# Contributor: Guoyi Zhang <guoyizhang at malacology dot net> _pkgname=fgsea _pkgver=1.26.0 pkgname=r-${_pkgname,,} -pkgver=1.26.0 -pkgrel=3 -pkgdesc='Fast Gene Set Enrichment Analysis' -arch=('x86_64') +pkgver=${_pkgver//-/.} +pkgrel=4 +pkgdesc="Fast Gene Set Enrichment Analysis" +arch=(x86_64) url="https://bioconductor.org/packages/${_pkgname}" -license=('MIT') +license=(MIT) depends=( - gcc - r - r-bh r-biocparallel r-cowplot r-data.table @@ -22,6 +19,15 @@ depends=( r-rcpp r-scales ) +makedepends=( + r-bh +) +checkdepends=( + r-geoquery + r-limma + r-reactome.db + r-testthat +) optdepends=( r-aggregation r-annotationdbi @@ -30,22 +36,29 @@ optdepends=( r-limma r-msigdbr r-org.mm.eg.db - r-parallel r-reactome.db r-rmarkdown r-seurat r-testthat ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('3b02276027800535421f38bbe5e83921') sha256sums=('ffd44dcf4e4a757ae4c79f3df99897a3e126fbca3e54457ace2c8cc923cf1632') 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" NOT_CRAN=true Rscript --vanilla testthat.R } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENCE" -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/LICENCE" "$pkgdir/usr/share/licenses/$pkgname" } -# vim:set ts=2 sw=2 et: |