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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=DOSE
_pkgver=3.28.2
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Disease Ontology Semantic and Enrichment analysis"
arch=(any)
url="https://bioconductor.org/packages/${_pkgname}"
license=(Artistic2.0)
depends=(
r-annotationdbi
r-biocparallel
r-fgsea
r-ggplot2
r-gosemsim
r-hdo.db
r-qvalue
r-reshape2
r-yulab.utils
)
checkdepends=(
r-testthat
)
optdepends=(
r-clusterprofiler
r-gson
r-hpo.db
r-knitr
r-mpo.db
r-org.hs.eg.db
r-prettydoc
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('db9c95935ce192a915b1246380f625d5')
sha256sums=('ee22b726664304643116a88c40eb8b2032e2a4faa92c2b2523986ddf19a2644e')
build() {
mkdir -p build
R CMD INSTALL "$_pkgname" -l build
}
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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