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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=magpie
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-annotationdbi
r-aod
r-biocparallel
r-deseq2
r-genomicfeatures
r-genomicranges
r-iranges
r-matrixstats
r-openxlsx
r-rcolorbrewer
r-reshape2
r-rsamtools
r-rtracklayer
r-s4vectors
r-tress
)
checkdepends=(
r-biocgenerics
r-runit
r-tbx20bamsubset
)
optdepends=(
r-biocgenerics
r-biocstyle
r-kableextra
r-knitr
r-rmarkdown
r-runit
r-tbx20bamsubset
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('a2d8cace71fdb5936f5e1eda05cf9989')
b2sums=('ea3f23eda8bb8e197d4ffb86eafa337ec8a950f2a2a20f054ce48ff1b7a6f2aa2d562ff849b1b16ee0afb7be1f518491513a29228e6e0d810ba732de9c6a3702')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" Rscript --vanilla runTest.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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