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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=oncoscanR
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Secondary analyses of CNV data (HRD and more)"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-genomicranges
r-iranges
r-magrittr
r-readr
r-s4vectors
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-jsonlite
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('41a3ad0c018823770001a20a8a1625ac')
b2sums=('391cb89f72d68aea4f4162efcb9e9570fc24471dc4880e5c2d5c7558c1a05708d1ae4cbcd2995df79750af52d88051e909163dccacb6b4a7ea7f07a8a7d0cf19')
build() {
mkdir build
R CMD INSTALL -l build "$_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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