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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=HiCExperiment
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Bioconductor class for interacting with Hi-C files in R"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biocgenerics
r-biocio
r-biocparallel
r-dplyr
r-genomeinfodb
r-genomicranges
r-interactionset
r-iranges
r-rhdf5
r-s4vectors
r-strawr
r-vroom
)
checkdepends=(
r-hicontactsdata
r-testthat
)
optdepends=(
r-biocfilecache
r-biocstyle
r-hicontacts
r-hicontactsdata
r-knitr
r-rmarkdown
r-rtracklayer
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('76c01f658236fe7e31800a0f58d59ef2')
b2sums=('4ae5fd100963ec83dd28cf7cc3da1cbeada5d7be29aa18980534be685db579858081f6ad60c844b3f1d1eab8c70659d53686d5056383d66046402329206d632f')
build() {
mkdir build
R CMD INSTALL -l build "$_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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