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78 lines
1.6 KiB
Bash
78 lines
1.6 KiB
Bash
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
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# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
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_pkgname=flowWorkspace
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_pkgver=4.12.2
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pkgname=r-${_pkgname,,}
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pkgver=${_pkgver//-/.}
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pkgrel=2
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pkgdesc="Infrastructure for representing and interacting with gated and ungated cytometry data sets."
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arch=(x86_64)
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url="https://bioconductor.org/packages/${_pkgname}"
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license=(AGPL3)
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depends=(
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boost-libs
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hdf5
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r-biobase
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r-biocgenerics
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r-cytolib
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r-data.table
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r-delayedarray
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r-dplyr
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r-flowcore
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r-ggplot2
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r-graph
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r-matrixstats
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r-ncdfflow
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r-rbgl
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r-rgraphviz
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r-rprotobuflib
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r-s4vectors
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r-scales
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r-xml
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)
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makedepends=(
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boost
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r-bh
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r-cpp11
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r-rhdf5lib
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)
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checkdepends=(
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r-flowworkspacedata
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r-testthat
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)
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optdepends=(
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r-cytoml
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r-flowworkspacedata
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r-ggcyto
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r-knitr
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r-opencyto
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r-rmarkdown
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r-testthat
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
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"system-hdf5.patch")
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md5sums=('ebb419044d24661c7b907e6fbf15ee60'
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'6074f63c3e946d2bdb0688a866a6271d')
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sha256sums=('46f42e329a43c48f9f8091ee114e889f0fa6beefd63a43f6f14f7bab44f530bc'
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'5bd4f81d4c8e4596a6f16d3d8040228228f5235bb5fb3a1baf363aee44251cee')
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prepare() {
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# use system hdf5 and skip failing tests
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patch -Np1 -i system-hdf5.patch
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}
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build() {
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mkdir -p build
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R CMD INSTALL "$_pkgname" -l build
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}
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check() {
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cd "$_pkgname/tests"
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R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
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}
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package() {
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install -d "$pkgdir/usr/lib/R/library"
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cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
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}
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