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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=katdetectr
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Detection, Characterization and Visualization of Kataegis in Sequencing Data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-biobase
r-biocparallel
r-bsgenome
r-bsgenome.hsapiens.ucsc.hg19
r-bsgenome.hsapiens.ucsc.hg38
r-changepoint
r-changepoint.np
r-checkmate
r-dplyr
r-genomeinfodb
r-genomicranges
r-ggplot2
r-ggtext
r-iranges
r-maftools
r-plyranges
r-rdpack
r-rlang
r-s4vectors
r-scales
r-tibble
r-tidyr
r-variantannotation
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('124d4211cd903a5c4e0a461a243c261a')
b2sums=('3737772a3b68cd8f7ccb3c7ec29728b98f5f3048a66b44f7f7b80d372833a8ce02ba29fd81f5cc6f5d48a3405b5f5d6b8918c224a490a39ace9e467319ec2115')
build() {
mkdir build
R CMD INSTALL -l build "$_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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