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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=speckle
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Statistical methods for analysing single cell RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-edger
r-ggplot2
r-limma
r-seurat
r-singlecellexperiment
)
checkdepends=(
r-testthat
r-vdiffr
)
optdepends=(
r-biocstyle
r-cellbench
r-jsonlite
r-knitr
r-patchwork
r-rmarkdown
r-scater
r-statmod
r-testthat
r-vdiffr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('d96d04d5338171fa9e2a2213a39fe729'
'8af9b352ae92d11644cae8af98be635a')
b2sums=('64d7333a2d92594dddefd2527cd1b18144888abfae7da66f276b1f646010863eca1494aa788370e7a7b0bd62338ecd8b47063b15d3494452248a777b53f513fe'
'3675d038b8f1a3df4a57c6227608bec986efcc0b8a551f1a5aec33cdcd19573c37c9f5ea2a7bdd37585187d6c8fd25c6cc849b9d5abad51e3d73bebec7af16c5')
prepare() {
# fix test snapshots
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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