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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=raer
_pkgver=1.0.2
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}_${_pkgver}.tar.gz")
md5sums=('da2d27f76962c7d534f36f05815670d3')
b2sums=('0079593d5d24b9500788c10e025364972d4d8d0f8eede7ee58a8ace5e9bb0d2f83cdbe89b377936bb855c0302662c82c340a3026ba82266034c380578021a1fa')
build() {
mkdir build
R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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