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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=gDNAx
_pkgver=1.0.0
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/${_pkgname}"
license=(Artistic2.0)
depends=(
r-annotationdbi
r-annotationhub
r-biocgenerics
r-biocparallel
r-biostrings
r-bitops
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicfiles
r-genomicranges
r-iranges
r-plotrix
r-rcolorbrewer
r-rsamtools
r-s4vectors
r-summarizedexperiment
)
checkdepends=(
r-gdnainrnaseqdata
r-runit
r-txdb.hsapiens.ucsc.hg38.knowngene
)
optdepends=(
r-biocstyle
r-gdnainrnaseqdata
r-knitr
r-rmarkdown
r-runit
r-txdb.hsapiens.ucsc.hg38.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('ca3a7370388bf64ba5ccae7161c64ebd')
sha256sums=('4b8c512d18a57fbddfe7f4625ca00e6f6d64eab31c7871a748fec7d2446aff5d')
build() {
mkdir -p build
R CMD INSTALL "$_pkgname" -l build
}
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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