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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=raer
_pkgver=1.0.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="RNA editing tools in R"
arch=(x86_64)
url="https://bioconductor.org/packages/${_pkgname}"
license=(MIT)
depends=(
curl
r-biocgenerics
r-biocparallel
r-biostrings
r-bsgenome
r-cli
r-data.table
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicranges
r-iranges
r-r.utils
r-rsamtools
r-rtracklayer
r-s4vectors
r-singlecellexperiment
r-summarizedexperiment
)
makedepends=(
r-rhtslib
)
checkdepends=(
r-edger
r-testthat
)
optdepends=(
r-annotationhub
r-biocstyle
r-bsgenome.hsapiens.ncbi.grch38
r-complexheatmap
r-covr
r-deseq2
r-edger
r-knitr
r-limma
r-raerdata
r-rmarkdown
r-scater
r-scran
r-scuttle
r-snplocs.hsapiens.dbsnp144.grch38
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('0b5c050626ce21756f90b4f9c967465b')
sha256sums=('4607eee1ad03f81724d7feae469236b6f7646831309eff928a6bbd9e7e7d8ce9')
build() {
mkdir -p build
R CMD INSTALL "$_pkgname" -l build
}
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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