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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=ORFik
_pkgver=1.26.2
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Open Reading Frames in Genomics"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-annotationdbi
r-biocfilecache
r-biocgenerics
r-biocparallel
r-biomart
r-biomartr
r-biostrings
r-bsgenome
r-cowplot
r-data.table
r-deseq2
r-fst
r-genomeinfodb
r-genomicalignments
r-genomicfeatures
r-genomicranges
r-ggplot2
r-gridextra
r-httr
r-iranges
r-jsonlite
r-r.utils
r-rcpp
r-rsamtools
r-rtracklayer
r-s4vectors
r-summarizedexperiment
r-txdbmaker
r-withr
r-xml
r-xml2
)
optdepends=(
r-biocstyle
r-bsgenome.hsapiens.ucsc.hg19
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('1a2c8f6a3d88637642f4cd5ade2214e6')
b2sums=('012f762fa66287eaa182e9dfe67333de2081401992b34e68b2c8ee2f7c1a7a5cc333650b30f55cb72cdf6c70ec514fc1e3ea1ea5f847348c9905f5ea4fb51afb')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
package() {
install -d "$pkgdir/usr/lib/R/library"
cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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