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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=screenCounter
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Counting Reads in High-Throughput Sequencing Screens"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biocparallel
r-rcpp
r-s4vectors
r-summarizedexperiment
r-zlibbioc
zlib
)
checkdepends=(
r-biostrings
r-testthat
)
optdepends=(
r-biocgenerics
r-biocstyle
r-biostrings
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('d41c087a96de1282f0ef7ebba97eba21')
b2sums=('6cbb46731b53438e724ac2b4df75e03a2be4744b70b97538327d70e734bb31adc077a029fd3f34a18359093fa311e8c9d224c437ecf725a7a5b5b94203edbd3d')
build() {
mkdir build
R CMD INSTALL -l build "$_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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