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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=GenomicDataCommons
_pkgver=1.26.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="NIH / NCI Genomic Data Commons Access"
arch=(any)
url="https://bioconductor.org/packages/${_pkgname}"
license=(Artistic2.0)
depends=(
r-dplyr
r-genomicranges
r-httr
r-iranges
r-jsonlite
r-magrittr
r-rappdirs
r-readr
r-rlang
r-tibble
r-tidyr
r-xml2
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocparallel
r-biocstyle
r-data.table
r-dt
r-genomicalignments
r-ggplot2
r-knitr
r-listviewer
r-maftools
r-r.utils
r-rmarkdown
r-rsamtools
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
r-variantannotation
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('6c945795f62ce3e0b470b07b892d3357')
sha256sums=('bc54fdafd609f40a2b2cd598e332b2611d377b4c3d1aa20c345bc1f9199bd1c6')
build() {
mkdir -p build
R CMD INSTALL "$_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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