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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
_pkgname=Rhisat2
_pkgver=1.20.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="R Wrapper for HISAT2 Aligner"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-genomicranges
r-sgseq
r-txdbmaker
)
optdepends=(
r-biocstyle
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-build.patch")
md5sums=('40eeced68deeadf6506e97eb53e4a831'
'3f45bc291d0db4e626db5336680b2f73')
b2sums=('f289e764d5085458a8248154e2aa8bc790c76c3e23866153757ba5e86a157b62b1d20f65732952a6a7fd0a8098b3c8289afcdd043c54fb691e69673fc07c35e0'
'f3d4cc8719124604b7d295c6143d38187901cbca50da949f4c49edac0d43e818cde3ab03cc05ad77425091db705979b1d9b381c751c0fada90b48796b54fee2c')
prepare() {
# fix compiler flags
patch -Np1 -i fix-build.patch
}
build() {
mkdir build
# parallel compilation fails
MAKEFLAGS+=" -j1"
R CMD INSTALL -l build "$_pkgname"
}
package() {
install -d "$pkgdir/usr/lib/R/library"
cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
}
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