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# Maintainer: peippo <christoph+aur@christophfink.com>
# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
# Contributor: Grey Christoforo <first name at last name dot net>
_bcname=GenomicRanges
_bcver=1.54.1
pkgname=r-${_bcname,,}
pkgdesc="Representation and manipulation of genomic intervals"
url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
pkgver=${_bcver//[:-]/.}
pkgrel=1
arch=("i686" "x86_64")
license=("Artistic2.0")
depends=(
"r>=4.0.0"
"r-biocgenerics>=0.37.0"
"r-genomeinfodb>=1.15.2"
"r-iranges>=2.31.2"
"r-s4vectors>=0.27.12"
"r-xvector>=0.29.2"
)
optdepends=(
"r-annotate"
"r-annotationdbi"
"r-annotationhub"
"r-biobase"
"r-biocstyle"
"r-biostrings>=2.25.3"
"r-bsgenome"
"r-bsgenome.hsapiens.ucsc.hg19"
"r-bsgenome.mmusculus.ucsc.mm10"
"r-bsgenome.scerevisiae.ucsc.saccer2"
"r-deseq2"
"r-dexseq"
"r-digest"
"r-edger"
"r-genomicalignments"
"r-genomicfeatures"
"r-gviz"
"r-hgu95av2.db"
"r-hgu95av2probe"
"r-kegggraph"
"r-keggrest"
"r-knitr"
"r-pasillabamsubset"
"r-rmarkdown"
"r-rnaseqdata.hnrnpc.bam.chr14"
"r-rsamtools>=1.13.53"
"r-rtracklayer"
"r-runit"
"r-summarizedexperiment>=0.1.5"
"r-txdb.athaliana.biomart.plantsmart22"
"r-txdb.dmelanogaster.ucsc.dm3.ensgene"
"r-txdb.hsapiens.ucsc.hg19.knowngene"
"r-txdb.mmusculus.ucsc.mm10.knowngene"
"r-variantannotation"
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
b2sums=('d08b113f0f0afbcf154f91f582d4d91f8c97c79567ecd8993cc4ff2b1a3f63d62026b9c6c457b17f6fd470c82b73431a1a2a46508ed7062d5332c7146e881cb9')
build() {
R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}"
}
package() {
install -dm0755 "${pkgdir}/usr/lib/R/library"
cp -a --no-preserve=ownership "${_bcname}" "${pkgdir}/usr/lib/R/library"
if [[ -f "${_bcname}/LICENSE" ]]; then
install -Dm0644 "${_bcname}/LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
fi
}
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