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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=mariner
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgdesc="Explore the Hi-Cs"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=(GPL3)
depends=(
r-abind
r-assertthat
r-biocgenerics
r-biocmanager
r-biocparallel
r-colourvalues
r-data.table
r-dbscan
r-delayedarray
r-genomeinfodb
r-genomicranges
r-glue
r-hdf5array
r-interactionset
r-iranges
r-magrittr
r-plotgardener
r-plyranges
r-progress
r-purrr
r-rcolorbrewer
r-rhdf5
r-rlang
r-s4vectors
r-strawr
r-summarizedexperiment
)
checkdepends=(
r-marinerdata
r-testthat
)
optdepends=(
r-dplyr
r-experimenthub
r-knitr
r-marinerdata
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-test-snapshot.patch")
md5sums=('6ed30878d03b8a17e8e7c4ee17218893'
'd0928c3ea11234e2200f31c9b4ff4ade')
b2sums=('dfaa195e26df395d9948668e342bcc5bc2c593d42b102a7140cb6778fc904f171b561c7fe1d6bce1dbefbd22832b745888549f06eff42c5596455d48e2693db3'
'aba583ffb72fea9e7ce5820b8160418b345b87e1d93fe9533efeb5732011373bd18dfea4c16b49f869e0d698529f48f738bec528c77d67c1cf095e7656a6ca30')
prepare() {
# fix snapshot test
patch -Np1 -i fix-test-snapshot.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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