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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=IgGeneUsage
_pkgver=1.18.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Differential gene usage in immune repertoires"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
onetbb
r-rcpp
r-rcppparallel
r-reshape2
r-rstan
r-rstantools
r-summarizedexperiment
r-tidyr
)
makedepends=(
r-bh
r-rcppeigen
r-stanheaders
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-ggforce
r-ggplot2
r-ggrepel
r-knitr
r-patchwork
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('6b09f356086c2d9d212b6b64973d69a9')
b2sums=('fa24145aaf622951e6439e2ee8859e7ce3cf5f133be0ff1828a46bbede22d787cf6af5b689cc33244d70bdf308d60e9470f1d130879bfa74eeb9d45245d4eaf6')
build() {
mkdir build
# compilation needs a lot of memory
MAKEFLAGS+=" -j1"
R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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