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73 lines
1.7 KiB
Bash
73 lines
1.7 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=CoGAPS
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_pkgver=3.22.0
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pkgname=r-${_pkgname,,}
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pkgver=${_pkgver//-/.}
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pkgrel=1
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pkgdesc="Coordinated Gene Activity in Pattern Sets"
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arch=(x86_64)
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url="https://bioconductor.org/packages/$_pkgname"
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license=('BSD-3-Clause')
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depends=(
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r-biocparallel
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r-biomart
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r-dplyr
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r-fgsea
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r-forcats
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r-ggplot2
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r-gplots
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r-msigdbr
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r-rcolorbrewer
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r-rcpp
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r-rhdf5
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r-s4vectors
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r-singlecellexperiment
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r-summarizedexperiment
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)
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makedepends=(
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r-bh
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)
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checkdepends=(
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r-testthat
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)
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optdepends=(
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r-biocstyle
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r-knitr
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r-rmarkdown
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r-seuratobject
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r-testthat
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
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"fix-openmp.patch")
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md5sums=('d4c9ec9b2be6c77fbb47c632b62c84b4'
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'7bbd2f800d95d2a4a9c81526b637e772')
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b2sums=('7836a9b7c52afb7fc009e7f49af2f4f59908c39bc20e77c3a1de72419d9f7a13c7d750f43c57429ca020d139ff0b0c96a5be61eb65c5a8f38f2546ce5c8db883'
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'1c794cab3dab46e4e50461c0d533f3a524940210dee7b27662421082a9f198e0faa7286a1d441299857cb064940a88f24767d88c1988216c22c330c97605737e')
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prepare() {
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# fix OpenMP
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patch -Np1 -i fix-openmp.patch
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cd "$_pkgname"
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autoupdate
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autoconf
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}
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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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install -d "$pkgdir/usr/share/licenses/$pkgname"
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ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
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}
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