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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=txdbmaker
_pkgver=1.0.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Tools for making TxDb objects from genomic annotations"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-annotationdbi
r-biobase
r-biocgenerics
r-biocio
r-biomart
r-dbi
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-httr
r-iranges
r-rjson
r-rsqlite
r-rtracklayer
r-s4vectors
r-ucsc.utils
)
checkdepends=(
r-rmariadb
r-runit
)
optdepends=(
r-biocstyle
r-ensembldb
r-knitr
r-mirbase.db
r-rmariadb
r-runit
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('d2145305fc78518240d1d9cace6478b1')
b2sums=('72f341676a93374d1f77c09a6cef707e54b102b5aea58e097e89144ef1389e3f15d8e051176e9a88a75645079e0da4704da354e5a7b3b7f49cd3b79053769263')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" Rscript --vanilla run_unitTests.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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