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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=HiContacts
_pkgver=1.14.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Analysing cool files in R with HiContacts"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biocgenerics
r-biocio
r-biocparallel
r-dplyr
r-genomeinfodb
r-genomicranges
r-ggplot2
r-ggrastr
r-hicexperiment
r-interactionset
r-iranges
r-readr
r-rspectra
r-s4vectors
r-scales
r-stringr
r-summarizedexperiment
r-tibble
r-tidyr
)
checkdepends=(
r-bsgenome.scerevisiae.ucsc.saccer3
r-hicontactsdata
r-rfast
r-testthat
r-wgcna
)
optdepends=(
r-biocstyle
r-biostrings
r-bsgenome.scerevisiae.ucsc.saccer3
r-genomicfeatures
r-hicontactsdata
r-knitr
r-patchwork
r-rfast
r-rmarkdown
r-rtracklayer
r-terra
r-testthat
r-wgcna
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('b2f0b879e1442e86902648997ee9cd96')
b2sums=('77006b94479cf489b9b0d49411adc1a9a2cab06e197f70460c52b0185d4fbbca7a0448105c338f8367012a2cc5de67999c7cec6e2b962a78c0d2fb6093f541b9')
build() {
mkdir build
R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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