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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=gDNAx
_pkgver=1.4.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Diagnostics for assessing genomic DNA contamination in RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-annotationdbi
r-annotationhub
r-biocgenerics
r-biocparallel
r-biostrings
r-bitops
r-cli
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicfiles
r-genomicranges
r-iranges
r-matrixstats
r-plotrix
r-rcolorbrewer
r-rsamtools
r-s4vectors
r-summarizedexperiment
)
checkdepends=(
r-gdnainrnaseqdata
r-runit
r-txdb.hsapiens.ucsc.hg38.knowngene
)
optdepends=(
r-biocstyle
r-gdnainrnaseqdata
r-knitr
r-rmarkdown
r-runit
r-txdb.hsapiens.ucsc.hg38.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('274f1f9cbd1e5ade86dd097682a3892c')
b2sums=('b3661b41c32803bb172e5bf42797a9c463d089c5e49023c9115d13b5fe81ce280cfa89ad77f7de012f9f0276f59538d3492e72abbf4143186e9e56cb75136c88')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" Rscript --vanilla runTests.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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