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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=RAIDS
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Accurate Inference of Genetic Ancestry from Cancer Sequences"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=(Apache)
depends=(
r-annotationdbi
r-annotationfilter
r-bsgenome
r-ensembldb
r-gdsfmt
r-genesis
r-genomicranges
r-iranges
r-matrixgenerics
r-proc
r-rlang
r-s4vectors
r-snprelate
r-variantannotation
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-bsgenome.hsapiens.ucsc.hg38
r-ensdb.hsapiens.v86
r-genomeinfodb
r-knitr
r-rmarkdown
r-testthat
r-withr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('68f024133092f72a434dd386f68b669c')
b2sums=('d8cf20407390fe537fd7419f8cc4f457ba67dde76c61c07ca603bd8f8b5c8722100e55666dca7925f73aa074124bfa3cf36b874944b251f57cb631b594681ad1')
build() {
mkdir build
R CMD INSTALL -l build "$_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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