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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=GenomeInfoDb
_bcver=1.42.1
pkgname="r-${_bcname,,}"
pkgver="${_bcver//[:-]/.}"
pkgrel=1
pkgdesc="Utilities for manipulating chromosome names, including modifying them to follow a particular naming style"
arch=("any")
url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
license=("Artistic-2.0")
depends=(
"r>=4.0.0"
"r-biocgenerics>=0.37.0"
"r-s4vectors>=0.25.12"
"r-iranges>=2.13.12"
"r-rcurl"
"r-genomeinfodbdata"
"r-ucsc.utils"
)
optdepends=(
"r-biocstyle"
"r-bsgenome"
"r-bsgenome.celegans.ucsc.ce2"
"r-bsgenome.hsapiens.ncbi.grch38"
"r-bsgenome.scerevisiae.ucsc.saccer2"
"r-data.table"
"r-genomicalignments"
"r-genomicfeatures"
"r-genomicranges"
"r-knitr"
"r-rsamtools"
"r-runit"
"r-txdb.dmelanogaster.ucsc.dm3.ensgene"
"r-r.utils"
)
# The unittests for `r-pkgcache` have circular
# dependency chains.
# As such, the tests can not be run on first build.
# While R packages from CRAN, generally, are well-tested
# before they are released, in some situations, you want to
# have thorough testing on your own end.
# To run the tests, first build this package without `check()`
# (i.e., as-is) to bootstrap `r-pkgcache`. Then, on subsequent builds,
# (assumining you have a local repository that is accessible from
# the build chroot), uncomment the lines defining `checkdepends`, below,
# as well as the `check()` function further down
# checkdepends=(
# "${optdepends[@]}"
# "r-rcmdcheck"
# )
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
b2sums=("d631d8ab803128b81bbeca8b3c03603208c09b9f92ee87f6f4c3d28cac0a9ed5b56ca268409be4236df0b2f17585a54578f363f58de3b9ed555b5b9b00aa7ce1")
build() {
mkdir -p "${srcdir}/build/"
R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}/build/"
}
# check() {
# cd "${srcdir}/${_bcname}/"
# R_LIBS="${srcdir}/build/" R CMD check --no-manual --no-multiarch --no-vignettes .
# }
package() {
install -dm0755 "${pkgdir}/usr/lib/R/library"
cp -a --no-preserve=ownership "${srcdir}/build/${_bcname}" "${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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