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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
# Contributor: Nick B <Shirakawasuna at gmail _dot_com>
_pkgname=flowCore
_pkgver=2.16.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Basic structures for flow cytometry data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-biobase
r-biocgenerics
r-cytolib
r-matrixstats
r-rcpp
r-s4vectors
)
makedepends=(
r-bh
r-cpp11
r-rprotobuflib
)
checkdepends=(
r-flowworkspacedata
r-testthat
)
optdepends=(
r-flowstats
r-flowviz
r-flowworkspace
r-flowworkspacedata
r-ggcyto
r-gridextra
r-knitr
r-opencyto
r-rgraphviz
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-build.patch")
md5sums=('a0d5745c70aeb16e1d1e9f4a65df2257'
'fc433793c9af520e6dcf2d9a5e40af4b')
b2sums=('6e95b80c05f074b849ebf3ce1dda7a978c5638946c23705d736d1f430f2233430efcffb987956337338eb4d5f267a7ba339e45e81f92493a458f7be8fb095e44'
'cf6f8d8d648cdd1cbfd0b37ab50e305b56e6fb1e0aa1cae15f56d6f714c51e4003e671611c77607396ea41dd5d282591bcf2e4483efa0d72c10d44042ab2f6b8')
prepare() {
# fix build and remove unnecessary import from tests
patch -Np1 -i fix-build.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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