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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=GeoTcgaData
_pkgver=2.0.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Processing Various Types of Data on GEO and TCGA"
arch=(any)
url="https://bioconductor.org/packages/${_pkgname}"
license=(Artistic2.0)
depends=(
r-cqn
r-data.table
r-plyr
r-summarizedexperiment
r-topconfects
)
checkdepends=(
r-clusterprofiler
r-edger
r-limma
r-org.hs.eg.db
r-testthat
)
optdepends=(
r-biocgenerics
r-catt
r-champ
r-clusterprofiler
r-dearseq
r-deseq2
r-edger
r-enrichplot
r-geoquery
r-illuminahumanmethylation450kanno.ilmn12.hg19
r-impute
r-knitr
r-limma
r-minfi
r-noiseq
r-org.hs.eg.db
r-quantreg
r-rmarkdown
r-s4vectors
r-tcgabiolinks
r-testthat
r-tidyr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('463ef0f64e092337495a3f6da55b224a')
sha256sums=('314062425c9e61fc002de591495c9fa57821fe8163c0e41542d7d0c14f4d6f39')
build() {
mkdir -p build
R CMD INSTALL "$_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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