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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=DNAfusion
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Identification of gene fusions using paired-end sequencing"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-bamsignals
r-biocbaseutils
r-biocgenerics
r-genomicalignments
r-genomicfeatures
r-genomicranges
r-iranges
r-rsamtools
r-s4vectors
r-txdb.hsapiens.ucsc.hg38.knowngene
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-rmarkdown
r-sessioninfo
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('b7ef2bb10bea5334d6d159208c284c16')
b2sums=('dd96d0d06ed4a162e894f24e9f0a759167279a23750b70e97732b5c9c5f4e388118c99aab1c405c36b1e99ffd7b8e269758e2b4b5bd80f3987f56b1cd5aa8d4c')
build() {
mkdir build
R CMD INSTALL -l build "$_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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