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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=gDNAx
_pkgver=1.2.1
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}_${_pkgver}.tar.gz")
md5sums=('dc325ba329126934b0850a4380af483d')
b2sums=('91c02ec63029ae9c408beae9fe164e476564d7933aadb6378bf9272ecc4c7827340c08a0d4a37bca4d9b6cb60d78cd8aa3ef396815f6c5c42ddc41d27d28dc56')
build() {
mkdir build
R CMD INSTALL -l build "$_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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