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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=BUSpaRse
_pkgver=1.18.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="kallisto | bustools R utilities"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('BSD-2-Clause')
depends=(
r-annotationdbi
r-annotationfilter
r-biocgenerics
r-biomart
r-biostrings
r-bsgenome
r-dplyr
r-ensembldb
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-ggplot2
r-iranges
r-magrittr
r-plyranges
r-rcpp
r-s4vectors
r-stringr
r-tibble
r-tidyr
r-zeallot
)
makedepends=(
r-bh
r-rcpparmadillo
r-rcppprogress
)
checkdepends=(
r-testthat
r-txdbmaker
)
optdepends=(
r-biocstyle
r-bsgenome.hsapiens.ucsc.hg38
r-ensdb.hsapiens.v86
r-knitr
r-rmarkdown
r-tenxbusdata
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
r-txdbmaker
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('5f9449a03f5fa044e500cb4808b1ae93')
b2sums=('f29e86c7bce91f5bc533bb513701badedec6ffab3774a69c86282a6dda78c8376cc034930a7a1e000ed2b4959caf53cb3c6212f2d49c749400cc84a45d0cb753')
build() {
mkdir build
R CMD INSTALL -l build "$_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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