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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=HumanTranscriptomeCompendium
_pkgver=1.17.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgdesc="Tools to work with a Compendium of 181000 human transcriptome sequencing studies"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-s4vectors
r-shiny
r-ssrch
r-summarizedexperiment
)
checkdepends=(
r-biocfilecache
r-biocmanager
r-rhdf5client
r-testthat
)
optdepends=(
r-beeswarm
r-biocfilecache
r-biocstyle
r-dplyr
r-dt
r-knitr
r-magrittr
r-rhdf5client
r-rmarkdown
r-testthat
r-tximport
r-tximportdata
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('00689fd704a35eea4e0ba38516603b49')
b2sums=('8b74cc6ea362178bd614539615e2fe6e1b5738dc7e22f534136c861a9fe59ef9442c04ccf4f5ae34fcbefb3eda9ff72376117ee710b27f3179d8f00c185f1b4a')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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