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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=BiocSingular
_pkgver=1.20.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Singular Value Decomposition for Bioconductor Packages"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-beachmat
r-biocgenerics
r-biocparallel
r-delayedarray
r-irlba
r-rcpp
r-rsvd
r-s4vectors
r-scaledmatrix
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-residualmatrix
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('d5a29e6d4dad421ec381313627270a0e')
b2sums=('53c788e4003bbb2fdf9880d430033f1bfe5dafe0e117e0e48e6ad5443c4fcd62716330b79563f3318c9ca39b10a62e7394f46cf597225d38c4b23a5e3399194a')
prepare() {
# skip test that makes a coredump
sed -i '/"scale calculations work correctly"/a\ \ \ \ skip("dumps core")' \
"$_pkgname/tests/testthat/test-utils.R"
}
build() {
mkdir 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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