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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=SpatialFeatureExperiment
_pkgver=1.6.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Integrating SpatialExperiment with Simple Features in sf"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-biobase
r-biocgenerics
r-biocneighbors
r-biocparallel
r-data.table
r-dropletutils
r-ebimage
r-lifecycle
r-rjson
r-rlang
r-s4vectors
r-sf
r-sfheaders
r-singlecellexperiment
r-spatialexperiment
r-spdep
r-summarizedexperiment
r-terra
r-zeallot
)
checkdepends=(
r-rbioformats
r-sfarrow
r-sfedata
r-testthat
r-xml2
)
optdepends=(
r-arrow
r-biocstyle
r-dplyr
r-knitr
r-rbioformats
r-rhdf5
r-rmarkdown
r-scater
r-seurat
r-seuratobject
r-sfarrow
r-sfedata
r-testthat
r-tidyr
r-voyager
r-xml2
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('ffdd8b3f445b1a9d5f5a8fe154f07c55'
'f291ecaed60ed25084e6b663457c1268')
b2sums=('db8b0d4007e1fad69c9bc66e57c127216f0662238d4f0a5bb7e72bb216d215ffd7abeb0ef7c5b39dd7eead16b2fddcdda04a44e9e39ca2ec4ac8d4780f978c5b'
'99ad8de9094bc321b6bfc2597ff1f9e06627a5cdb277fd0d1a5de5ecf76885b7163d00ea2f1fa9a6701cea0b4a5cea458f8a727c4f0dcadb5a493afd22940cc1')
prepare() {
# skip tests that require r-voyager
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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