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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=decontX
_pkgver=1.0.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Decontamination of single cell genomics data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
onetbb
r-celda
r-dbscan
r-delayedarray
r-ggplot2
r-mcmcprecision
r-patchwork
r-plyr
r-rcpp
r-rcppparallel
r-reshape2
r-rstan
r-rstantools
r-s4vectors
r-scater
r-seurat
r-singlecellexperiment
r-summarizedexperiment
r-withr
)
makedepends=(
r-bh
r-rcppeigen
r-stanheaders
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-dplyr
r-knitr
r-rmarkdown
r-scran
r-singlecellmultimodal
r-tenxpbmcdata
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('1e2f4af9204397b8104543dd954bb390')
b2sums=('f6083f5678fbaeb0676893f1a70d33946392b67d88902cb59202d083f5dd137d43e09f7dec92f8df3353c968283e018791a7c4075e2cf7f12c497425824fc152')
build() {
mkdir build
R CMD INSTALL -l build "$_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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