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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=spatialLIBD
_pkgver=1.16.2
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="an R/Bioconductor package to visualize spatially-resolved transcriptomics data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-annotationhub
r-benchmarkme
r-biocfilecache
r-biocgenerics
r-cowplot
r-dt
r-edger
r-experimenthub
r-fields
r-genomicranges
r-ggplot2
r-golem
r-iranges
r-jsonlite
r-limma
r-magick
r-matrixgenerics
r-paletteer
r-plotly
r-png
r-rcolorbrewer
r-rlang
r-rtracklayer
r-s4vectors
r-scater
r-scuttle
r-sessioninfo
r-shiny
r-shinywidgets
r-singlecellexperiment
r-spatialexperiment
r-statmod
r-summarizedexperiment
r-tibble
r-viridislite
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocmanager
r-biocstyle
r-covr
r-dropletutils
r-here
r-knitr
r-lobstr
r-refmanager
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('ad0807a9b15b57c60313c504fd908822'
'ff2fc6d00615921ec62383cabcea1afb')
b2sums=('06f3048b306f6440f6a60b6d231a3fc7e1cb9b4901ec005dd57602f7fe028f3f02c916a3cfb5a3a0e8c4289e39817a8901ba095e7ab0402617ecf0906cf5a0a3'
'637e4f2e31c0e77dfefacffd24c5e8a90b3bc70b36d68ec2fffebc41ca0bafe94707f02e67d42f22497d354a36b91157219d795661e80c173361fd33b20ae523')
prepare() {
# skip failing tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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