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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=katdetectr
_pkgver=1.8.0
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}_${_pkgver}.tar.gz")
md5sums=('b82e34bb3c3d447ca1899d32dd214f1d')
b2sums=('465184cf790a851c77d4f87f4eaa539c2c24e7adcd537e669e33ed5131217d64e34c02fd339ce3fdbf9aab79b04a106b38d066bb70e4935036a9b99a74c7c6a3')
build() {
mkdir build
R CMD INSTALL -l build "$_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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