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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=extraChIPs
_pkgver=1.8.5
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Additional functions for working with ChIP-Seq data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-biocio
r-biocparallel
r-broom
r-complexupset
r-csaw
r-dplyr
r-edger
r-forcats
r-genomeinfodb
r-genomicinteractions
r-genomicranges
r-ggforce
r-ggplot2
r-ggrepel
r-ggside
r-glue
r-interactionset
r-iranges
r-matrixstats
r-patchwork
r-rcolorbrewer
r-rlang
r-rsamtools
r-rtracklayer
r-s4vectors
r-scales
r-stringr
r-summarizedexperiment
r-tibble
r-tidyr
r-tidyselect
r-vctrs
r-venndiagram
)
checkdepends=(
r-apeglm
r-deseq2
r-enrichedheatmap
r-harmonicmeanp
r-testthat
)
optdepends=(
r-apeglm
r-biocstyle
r-covr
r-deseq2
r-enrichedheatmap
r-gviz
r-harmonicmeanp
r-here
r-knitr
r-limma
r-magrittr
r-plyranges
r-quantro
r-rmarkdown
r-testthat
r-tidyverse
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('d515730a24ba1c2498470f5640bf8a27')
b2sums=('f48b70df77b0ae1ecc3ffb6b6bb188f7bdcbc3f9dd4a88714b4bc63a7802fe470e74a546bc65140c4a2ceebd64550ae9b93b782e499e79c61568a32c6a5f6165')
build() {
mkdir build
R CMD INSTALL -l build "$_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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