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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=Seurat
_pkgver=5.0.2
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Tools for Single Cell Genomics"
arch=(x86_64)
url="https://cran.r-project.org/package=$_pkgname"
license=('MIT')
depends=(
r-cowplot
r-fastdummies
r-fitdistrplus
r-future
r-future.apply
r-generics
r-ggplot2
r-ggrepel
r-ggridges
r-httr
r-ica
r-igraph
r-irlba
r-jsonlite
r-leiden
r-lifecycle
r-lmtest
r-matrixstats
r-miniui
r-patchwork
r-pbapply
r-plotly
r-png
r-progressr
r-purrr
r-rann
r-rcolorbrewer
r-rcpp
r-rcppannoy
r-rcpphnsw
r-reticulate
r-rlang
r-rocr
r-rspectra
r-rtsne
r-scales
r-scattermore
r-sctransform
r-seuratobject
r-shiny
r-spatstat.explore
r-spatstat.geom
r-tibble
r-uwot
)
makedepends=(
r-rcppeigen
r-rcppprogress
)
checkdepends=(
r-glmgampoi
r-harmony
r-limma
r-singlecellexperiment
r-testthat
)
optdepends=(
r-ape
r-biobase
r-biocgenerics
r-bpcells
r-data.table
r-delayedarray
r-deseq2
r-enrichr
r-genomeinfodb
r-genomicranges
r-ggrastr
r-harmony
r-hdf5r
r-iranges
r-limma
r-mast
r-metap
r-mixtools
r-monocle
r-presto
r-r.utils
r-rfast2
r-rsvd
r-rtracklayer
r-s4vectors
r-singlecellexperiment
r-summarizedexperiment
r-testthat
r-vgam
)
source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('cb58cbc4b85dae89262c43f1d86c49ff')
b2sums=('bab400c3a6465734622d4439212e4cbd9d1324d949a75d4501b2f73bc20f6409a38fd509aa65049135253ffbf4940d332a2327fe5c5f8c43b5cca36fc2aae86a')
prepare() {
# skip test that requires BPCells
sed -i '/"pca is equivalent for BPCells"/a\ \ skip_if_not_installed("BPCells")' \
"$_pkgname/tests/testthat/test_dimensional_reduction.R"
}
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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