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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=SpotClean
_pkgver=1.10.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="SpotClean adjusts for spot swapping in spatial transcriptomics data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-dplyr
r-ggplot2
r-rcolorbrewer
r-readbitmap
r-rhdf5
r-rjson
r-rlang
r-s4vectors
r-seurat
r-spatialexperiment
r-summarizedexperiment
r-tibble
r-viridis
)
checkdepends=(
r-r.utils
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-r.utils
r-rmarkdown
r-spelling
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('9bef78613def9705e44d6eff87715f78')
b2sums=('a3f36371c3d0c248e46904954f26a0755c0ed22f8fece325eb7268fc788edeed77ca99ff316444ab619f423ebe3ac4d31bbeb1d2b229b0f2c894b398089f45f9')
build() {
mkdir build
R CMD INSTALL -l build "$_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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