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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=fgsea
_pkgver=1.30.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
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}_${_pkgver}.tar.gz")
md5sums=('ee0533776cc2027d55f81c5dca569464')
b2sums=('dbad9d4ce98cb10e61cc1036fb6f581c22957a91f43252e1cc98e2c3f827ca80cf447a8945694326804cb0abe0877f4a020ccd818f4f3d4e7435e01c3737e9a7')
build() {
mkdir build
R CMD INSTALL -l build "$_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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