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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=fgsea
_pkgver=1.28.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
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}_${_pkgver}.tar.gz")
md5sums=('53b8ab8a13390a0920bc13eeba3aa1b8')
b2sums=('a1c4a1c702f629084de6c8dd60f3094fc1fc1ff15df2c3d5319e9bd303cc247e7a5bc321123c9bff5364002035cb5cf19ae8b161e5869c76a0026fc97e90fe8a')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
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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