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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=CytoML
_pkgver=2.14.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="A GatingML Interface for Cross Platform Cytometry Data Sharing"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('AGPL-3.0-only')
depends=(
boost-libs
libxml2
r-biobase
r-cytolib
r-data.table
r-dplyr
r-flowcore
r-flowworkspace
r-ggcyto
r-graph
r-jsonlite
r-opencyto
r-rbgl
r-rgraphviz
r-tibble
r-xml
r-yaml
)
makedepends=(
boost
r-bh
r-cpp11
r-rhdf5lib
r-rprotobuflib
)
checkdepends=(
r-flowworkspacedata
r-testthat
)
optdepends=(
r-flowworkspacedata
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"system-hdf5.patch")
md5sums=('4b0060416cdeef7876cb9aaeb81dbaf7'
'c830342f553f0cfc7ac954ec93b429c2')
b2sums=('60eaf5dd32f6c2305b85c90c98100ec4d372a60fd5d3ed8d5d91c34c5cee76c4eccef11ce090dabb6c17243bcce3350ab0985889c0e940c4e58c0f636b8d190d'
'841b451423480c8a53debd7b63f5d83e27ffb064e2eff8051f284560f658cac1826fbf0172fad09aa3810f78e7a4cfd3ad41bdaf3fc28ec4c8d76ed2f418e666')
prepare() {
# use system hdf5
patch -Np1 -i system-hdf5.patch
}
build() {
mkdir build
R CMD INSTALL -l build "$_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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