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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=RNAmodR
_pkgver=1.18.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Detection of post-transcriptional modifications in high throughput sequencing data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-biocgenerics
r-biocparallel
r-biostrings
r-bsgenome
r-colorramps
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicranges
r-ggplot2
r-gviz
r-iranges
r-matrixstats
r-modstrings
r-rcolorbrewer
r-reshape2
r-rocr
r-rsamtools
r-rtracklayer
r-s4vectors
r-txdbmaker
)
checkdepends=(
r-rnamodr.data
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-rmarkdown
r-rnamodr.data
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('b7fedb35353258c8ab2c8915f0367283')
b2sums=('8fbf460349f3c6cd9c7e46e75c4564065654897742fbee3530c967ef356961064bb2aa468adbc4c2b86df515cab1ad298a679564ea35ddfaec10ddac22c35a00')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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