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75 lines
1.5 KiB
Bash
75 lines
1.5 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=compcodeR
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_pkgver=1.42.0
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pkgname=r-${_pkgname,,}
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pkgver=${_pkgver//-/.}
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pkgrel=1
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pkgdesc="RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods"
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arch=(any)
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url="https://bioconductor.org/packages/$_pkgname"
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license=('GPL-2.0-or-later')
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depends=(
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r-ape
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r-catools
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r-edger
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r-ggplot2
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r-gplots
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r-gtools
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r-knitr
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r-limma
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r-markdown
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r-matrixstats
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r-modeest
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r-phylolm
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r-rmarkdown
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r-rocr
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r-shiny
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r-shinydashboard
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r-sm
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r-stringr
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r-vioplot
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)
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checkdepends=(
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r-ggtree
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r-phangorn
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r-phytools
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r-testthat
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r-tidytree
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)
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optdepends=(
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r-biocstyle
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r-covr
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r-deseq2
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r-ebseq
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r-genefilter
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r-ggtree
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r-nbpseq
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r-noiseq
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r-phangorn
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r-phytools
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r-statmod
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r-sva
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r-tcc
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r-testthat
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r-tidytree
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
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md5sums=('ecec021bb3b146653a2ccd867faaa0b7')
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b2sums=('fd680644b9534b3ecbb771e61274a6622b376488d174fed47f67cf17e5ceab8190b9133cab6f2523c2d9107ff491fcde78578a38239c6c5bc18853b546faa1c9')
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build() {
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mkdir build
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R CMD INSTALL -l build "$_pkgname"
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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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