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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=pairedGSEA
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Paired DGE and DGS analysis for gene set enrichment analysis"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-aggregation
r-biocparallel
r-deseq2
r-dexseq
r-fgsea
r-ggplot2
r-limma
r-s4vectors
r-summarizedexperiment
r-sva
)
checkdepends=(
r-msigdbr
r-plotly
r-readr
r-testthat
r-writexl
)
optdepends=(
r-biocstyle
r-covr
r-knitr
r-msigdbr
r-plotly
r-readr
r-readxl
r-rhdf5
r-rmarkdown
r-testthat
r-writexl
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('2e2d1521409b95e8f06e73b8341b2749')
b2sums=('2d131331baa32956d6581b3353b75bd5e032f7e298ab9f2108c2318ede8e4785b7a3fad0e1869fafc9802324241872d2e0415dc3a7c5fc6f0349201e6c873050')
build() {
mkdir build
R CMD INSTALL -l build "$_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/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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