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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=oncoscanR
_pkgver=1.10.0
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}_${_pkgver}.tar.gz")
md5sums=('052581a13383556ad901cac871807c3c')
b2sums=('005b657ddefb6fadf2543f64d7d2a6c54404790d1f70be8ca88fa2edd16a85013f5872e08b9c75543d0ba5b4fbd04a8b645b841ab0b2e044a7968e7e7423ffc0')
build() {
mkdir build
R CMD INSTALL -l build "$_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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