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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=DNAfusion
_pkgver=1.14.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Identification of gene fusions using paired-end sequencing"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-biocbaseutils
r-biocgenerics
r-genomicalignments
r-genomicfeatures
r-genomicranges
r-iranges
r-rsamtools
r-s4vectors
r-txdb.hsapiens.ucsc.hg38.knowngene
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-rmarkdown
r-sessioninfo
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('6bb3ae0859f679e4e20ba2b7fbed3784')
b2sums=('83de6069571264e17edd45b48dc755913d8be34b84aa8d9aacf49a4be0a143f4795e5d96e6eb81cd876b06f17fda5b57e75631a67de60ff960f7f3386dae42d3')
build() {
mkdir build
R CMD INSTALL -l build "$_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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