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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=qsvaR
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Generate Quality Surrogate Variable Analysis for Degradation Correction"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-ggplot2
r-summarizedexperiment
r-sva
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocfilecache
r-biocstyle
r-covr
r-knitr
r-limma
r-refmanager
r-rmarkdown
r-sessioninfo
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('e9531cc164f93967a5d5d0469d47f7c7')
b2sums=('f8a5d4c27cebee2a429e2e2d566e348ea216c035957e78f965384545a587f1ba166b4142678d02d956e70a47f2ddb08b6b5adf4669eb8d31b4432150df8d2ea0')
build() {
mkdir build
R CMD INSTALL -l build "$_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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