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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=lineagespot
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-data.table
r-httr
r-matrixgenerics
r-stringr
r-summarizedexperiment
r-variantannotation
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-refmanager
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('774c39427111843ee37e6cb07d38aa65')
b2sums=('39d1997b025158202722f62fc44a5909ce69b532a873415d0e5fcb3668a4fb42a6be52ef85ab6f6b15be8d56fd393bdfa454c87aa925ad2c56e3fdd41f669a44')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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