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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=mariner
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Explore the Hi-Cs"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-abind
r-assertthat
r-biocgenerics
r-biocmanager
r-biocparallel
r-colourvalues
r-data.table
r-dbscan
r-delayedarray
r-genomeinfodb
r-genomicranges
r-glue
r-hdf5array
r-interactionset
r-iranges
r-magrittr
r-plotgardener
r-plyranges
r-progress
r-purrr
r-rcolorbrewer
r-rhdf5
r-rlang
r-s4vectors
r-strawr
r-summarizedexperiment
)
checkdepends=(
r-marinerdata
r-testthat
)
optdepends=(
r-dplyr
r-experimenthub
r-knitr
r-marinerdata
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-test-snapshot.patch")
md5sums=('59fce5faa48236d0a9cd9bdda6480d3d'
'b055713d876d7ea3e97a92a152bb5f28')
b2sums=('e2c553258972c7d24b907feab042be3fce9547636a6fbb1c264148002928b48fec581504e8281c214d076bdca3933eda08f9df6ad6f7b0d74d1e3847e8bee75f'
'6111457fda4b526e70b08ac62ec1ffd68dd8fe81d6d57cd715ef4f10a5156756d788043a924d9b3103958775cc28d02e0313947187a571907a9f6adf879148a1')
prepare() {
# fix snapshot test
patch -Np1 -i fix-test-snapshot.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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