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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=regioneReloaded
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Multiple Association for Genomic Region Sets"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-ggplot2
r-ggrepel
r-rcolorbrewer
r-regioner
r-reshape2
r-rtsne
r-scales
r-umap
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-genomeinfodb
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('b8efd6652c53bd1d591caf297f63e5ed'
'de0dc0c63b3a20635a3fe2e8d167d62c')
b2sums=('8c43517164de7ee7d3a462fdee988f2533670fe5e85cb28d9bbbef63ce4de9f9e34bf8c5f5a748319758a0f5641cc3b6f6197d0f6386ec572e225f35adb471b5'
'66966c7cbe3b17342b4e6cf0040f9ec46ea7569a74311c1f8da2f7f0152346512bae7062b24f0b72ba7c761c1e1746795bdbcc24d2a447028c8117d9daf4f257')
prepare() {
# fix tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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