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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=scGPS
_pkgver=1.20.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
blas
lapack
onetbb
r-caret
r-deseq2
r-dplyr
r-dynamictreecut
r-fastcluster
r-ggplot2
r-glmnet
r-locfit
r-rcpp
r-rcpparmadillo
r-rcppparallel
r-singlecellexperiment
r-summarizedexperiment
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocparallel
r-clusterprofiler
r-cowplot
r-dendextend
r-devtools
r-dose
r-e1071
r-knitr
r-networkd3
r-org.hs.eg.db
r-rcolorbrewer
r-reactomepa
r-reshape2
r-rmarkdown
r-rtsne
r-testthat
r-wgcna
r-xlsx
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-build.patch")
md5sums=('656578131e67e1f49507007d41c7c772'
'10f827551e2b78263235e157e5b6a4b2')
b2sums=('855cdd27c98aea038304eac62450cedec071fceccdba4dfc2b7badab2e1380688a2d622f008fbd2a299fb21661738e4ed9f5459b403162c3efb7bf09644ccc17'
'e2f840b1d0e9a8897ac8233ce695ea40e658797e01ad46f50bb5e7528efcf3797ec402b22c92d0b8a16c96bd7f4146664b81f9e7998525057426b61d05693e89')
prepare() {
# fix linking with onetbb
patch -Np1 -i fix-build.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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