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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=gatom
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Finding an Active Metabolic Module in Atom Transition Network"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-bionet
r-data.table
r-ggally
r-ggplot2
r-htmltools
r-htmlwidgets
r-igraph
r-intergraph
r-mwcsr
r-network
r-plyr
r-pryr
r-shinycyjs
r-sna
r-xml
)
checkdepends=(
r-org.mm.eg.db
r-reactome.db
r-testthat
)
optdepends=(
r-annotationdbi
r-biocstyle
r-fgsea
r-keggrest
r-knitr
r-org.mm.eg.db
r-r.utils
r-reactome.db
r-readr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('e3861da00bd8a76677fbef482690690c')
b2sums=('505051b52915ac697fbedeeb315d93af2a23cb3379219b52eff918cad86987cb8965f7ac46c8fed66cd8188530a9d2da3a1f231983e9222a546abc6bcef8305c')
build() {
mkdir build
R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENCE" "$pkgdir/usr/share/licenses/$pkgname"
}
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