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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=fgsea
_pkgver=1.26.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=4
pkgdesc="Fast Gene Set Enrichment Analysis"
arch=(x86_64)
url="https://bioconductor.org/packages/${_pkgname}"
license=(MIT)
depends=(
r-biocparallel
r-cowplot
r-data.table
r-fastmatch
r-ggplot2
r-rcpp
r-scales
)
makedepends=(
r-bh
)
checkdepends=(
r-geoquery
r-limma
r-reactome.db
r-testthat
)
optdepends=(
r-aggregation
r-annotationdbi
r-geoquery
r-knitr
r-limma
r-msigdbr
r-org.mm.eg.db
r-reactome.db
r-rmarkdown
r-seurat
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('3b02276027800535421f38bbe5e83921')
sha256sums=('ffd44dcf4e4a757ae4c79f3df99897a3e126fbca3e54457ace2c8cc923cf1632')
build() {
mkdir -p build
R CMD INSTALL "$_pkgname" -l build
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
}
package() {
install -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"
}
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