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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=hermes
_pkgver=1.10.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Preprocessing, analyzing, and reporting of RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Apache-2.0')
depends=(
r-assertthat
r-biobase
r-biocgenerics
r-biomart
r-checkmate
r-circlize
r-complexheatmap
r-deseq2
r-dplyr
r-edger
r-envstats
r-forcats
r-genomicranges
r-ggfortify
r-ggplot2
r-ggrepel
r-iranges
r-lifecycle
r-limma
r-magrittr
r-matrixstats
r-multiassayexperiment
r-purrr
r-r6
r-rdpack
r-rlang
r-s4vectors
r-summarizedexperiment
r-tidyr
)
checkdepends=(
r-testthat
r-vdiffr
)
optdepends=(
r-biocstyle
r-delayedarray
r-dt
r-httr
r-knitr
r-rmarkdown
r-statmod
r-testthat
r-vdiffr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('66f15d90a3af1663393f1904bbdd74f0'
'b913685944ab7f820abfa5d3fddc95ae')
b2sums=('87b5cd68db0eeb2994cba190ca76fb45e53c4907a477eb4f6057ab7832cfa6a4af5487a73f800207babfe4012f7542cc973aa942e03d1e305a79b692b4e9c183'
'b6de64020a5beea8add0fcf55e1389ca8404fcb0ee8bbb7260966ca2a6062c8e94c79f4d0964234fb6fe379b26fa15b426d51e59fd724560b0f954b2072e7106')
prepare() {
# fix snapshot tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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