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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>

_pkgname=IgGeneUsage
_pkgver=1.16.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Differential gene usage in immune repertoires"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
  onetbb
  r-rcpp
  r-rcppparallel
  r-reshape2
  r-rstan
  r-rstantools
  r-summarizedexperiment
  r-tidyr
)
makedepends=(
  r-bh
  r-rcppeigen
  r-stanheaders
)
checkdepends=(
  r-testthat
)
optdepends=(
  r-biocstyle
  r-ggforce
  r-ggplot2
  r-ggrepel
  r-gridextra
  r-knitr
  r-rmarkdown
  r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('231f1af3465f435ca3bb099a93e51e5b')
b2sums=('6b645f318f8017a9ca973f869b5924899aaf39262e46e920d7757c8361d847ac4c623811df25dfbbeb12087fca01875edd6bbc84d2989c0d381f5e3c6bb6ed35')

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"

  install -d "$pkgdir/usr/share/licenses/$pkgname"
  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}