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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=nnSVG
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Scalable identification of spatially variable genes in spatially-resolved transcriptomics data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biocparallel
r-brisc
r-matrixstats
r-singlecellexperiment
r-spatialexperiment
r-summarizedexperiment
)
checkdepends=(
r-scran
r-stexampledata
r-testthat
)
optdepends=(
r-biocstyle
r-ggplot2
r-knitr
r-rmarkdown
r-scran
r-stexampledata
r-testthat
r-weberdivechalcdata
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('24adcb1712b14cf817e92590762ed6be'
'41ab7394f6ddcf0b0751e14cbe78b1d1')
b2sums=('f5e894d5bb9553f5dbcca9558d49622d2e0bfc4ca1e66247aebf4c27a749377a39cf959b3f2575379315968813005c87c37d64fcf6b8b4fb5dd90553dfad91f5'
'c586a59926aad5469e9ea58861829cd70326cb0023b28e8b814df2cdcc6efb1636fbcf548fcf561d19d6e7b4f2356a6d7a29b1cb9fc2bffdf2b1de45737d3c5a')
prepare() {
# skip failing tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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