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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=seqminer
_pkgver=9.4
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R"
arch=(x86_64)
url="https://cran.r-project.org/package=$_pkgname"
license=('GPL-2.0-or-later AND MIT')
depends=(
bzip2
r
sqlite
zlib
zstd
)
checkdepends=(
r-testthat
)
optdepends=(
r-skat
r-testthat
)
source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('5922d7a82037e970121b8b31df2c53cc')
b2sums=('1228b1c94b1d7157a2f031b34f7ccd26a9a8ad58bfae29c78d22ad59bfd40c0d9227719be8613cd87d6e7ba963e0e6b84f28bbd67d0566422c3b58ddcac03138')
build() {
mkdir build
R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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