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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=BiocSingular
_pkgver=1.18.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Singular Value Decomposition for Bioconductor Packages"
arch=(x86_64)
url="https://bioconductor.org/packages/${_pkgname}"
license=(GPL3)
depends=(
r-beachmat
r-biocgenerics
r-biocparallel
r-delayedarray
r-irlba
r-rcpp
r-rsvd
r-s4vectors
r-scaledmatrix
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-residualmatrix
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('9b4158e143f2cbefc140228c13090b35')
sha256sums=('634824a2e15c13c9fefbb17605a3861bdced6fc182c8880ae862f2248600377c')
prepare() {
# skip test that makes a coredump
sed -i '/"scale calculations work correctly"/a\ \ \ \ skip("dumps core")' \
"$_pkgname/tests/testthat/test-utils.R"
}
build() {
mkdir -p build
R CMD INSTALL "$_pkgname" -l build
}
check() {
cd "$_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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