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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=hermes
_pkgver=1.6.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Preprocessing, analyzing, and reporting of RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Apache-2.0')
depends=(
r-assertthat
r-biobase
r-biocgenerics
r-biomart
r-checkmate
r-circlize
r-complexheatmap
r-deseq2
r-dplyr
r-edger
r-envstats
r-forcats
r-genomicranges
r-ggfortify
r-ggplot2
r-ggrepel
r-iranges
r-lifecycle
r-limma
r-magrittr
r-matrixstats
r-multiassayexperiment
r-purrr
r-r6
r-rdpack
r-rlang
r-s4vectors
r-summarizedexperiment
r-tidyr
)
checkdepends=(
r-testthat
r-vdiffr
)
optdepends=(
r-biocstyle
r-delayedarray
r-dt
r-httr
r-knitr
r-rmarkdown
r-statmod
r-testthat
r-vdiffr
r-withr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"skip-tests.patch")
md5sums=('9e758f81455d5fc7a8b57c3a65b4de5b'
'e228515b639417bea13853cfc94b866a')
b2sums=('224fd9ad63e1bdf566a41e58f90c2cd120008add812f0ff4e777d72d9c3896c7d7ed06b5759b5c5330b2126dfc0cb6097584c7650c8a1f12fd2c1dcdf34ed99c'
'b781820238d74265dce64de9804bd568587c61c0460e15b32eabf27e0f827d673e52e852274e2613a2cf55bd54e218ad21493d78fc16f8fe954a98d3b9970bb7')
prepare() {
# skip failing tests
patch -Np1 -i skip-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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