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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=SARC
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Statistical Analysis of Regions with CNVs"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-data.table
r-desctools
r-genomicfeatures
r-genomicranges
r-ggplot2
r-gridextra
r-gtable
r-iranges
r-metap
r-multtest
r-plotly
r-plyranges
r-raggedexperiment
r-rcolorbrewer
r-reshape2
r-scales
r-tidyverse
)
checkdepends=(
r-homo.sapiens
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
)
optdepends=(
r-genomicalignments
r-homo.sapiens
r-kableextra
r-knitr
r-mus.musculus
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
r-txdb.mmusculus.ucsc.mm10.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('c9049814349b5f868bd9415d032e70b1')
b2sums=('4a53269c55e8015f353025591cfc1d096916898778376bdd1b6d125004c9bb40428d93bbd7ff14e5f9f45a3bd9f7e4499e4939a4f5ba38f0e3caad31b3a863e7')
build() {
mkdir build
R CMD INSTALL -l build "$_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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