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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=simona
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc='Semantic Similarity on Bio-Ontologies'
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
java-runtime
perl
r-circlize
r-complexheatmap
r-getoptlong
r-globaloptions
r-igraph
r-matrixstats
r-polychrome
r-rcpp
r-s4vectors
r-shiny
r-xml2
)
checkdepends=(
r-go.db
r-org.hs.eg.db
r-proxyc
r-testthat
)
optdepends=(
r-annotationdbi
r-annotationhub
r-biocmanager
r-diagrammer
r-go.db
r-interactivecomplexheatmap
r-jsonlite
r-knitr
r-org.hs.eg.db
r-png
r-proxyc
r-ragg
r-simplifyenrichment
r-testthat
r-uniprotkeywords
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('0ec4ab17b45b0e4e753a9e3507a76360')
b2sums=('37944f78282569739c984b1ad2e7957656d4180380af08433c973434d6a3f87facbbe59cef3b7c270327f44e3775ecf986f0a14d1b291ec72593a4a9551b6114')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla test-all.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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