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83 lines
1.7 KiB
Bash
83 lines
1.7 KiB
Bash
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
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_pkgname=hermes
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_pkgver=1.10.0
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pkgname=r-${_pkgname,,}
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pkgver=${_pkgver//-/.}
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pkgrel=1
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pkgdesc="Preprocessing, analyzing, and reporting of RNA-seq data"
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arch=(any)
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url="https://bioconductor.org/packages/$_pkgname"
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license=('Apache-2.0')
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depends=(
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r-assertthat
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r-biobase
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r-biocgenerics
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r-biomart
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r-checkmate
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r-circlize
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r-complexheatmap
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r-deseq2
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r-dplyr
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r-edger
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r-envstats
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r-forcats
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r-genomicranges
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r-ggfortify
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r-ggplot2
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r-ggrepel
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r-iranges
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r-lifecycle
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r-limma
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r-magrittr
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r-matrixstats
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r-multiassayexperiment
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r-purrr
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r-r6
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r-rdpack
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r-rlang
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r-s4vectors
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r-summarizedexperiment
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r-tidyr
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)
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checkdepends=(
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r-testthat
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r-vdiffr
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)
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optdepends=(
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r-biocstyle
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r-delayedarray
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r-dt
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r-httr
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r-knitr
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r-rmarkdown
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r-statmod
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r-testthat
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r-vdiffr
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
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"fix-tests.patch")
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md5sums=('66f15d90a3af1663393f1904bbdd74f0'
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'b913685944ab7f820abfa5d3fddc95ae')
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b2sums=('87b5cd68db0eeb2994cba190ca76fb45e53c4907a477eb4f6057ab7832cfa6a4af5487a73f800207babfe4012f7542cc973aa942e03d1e305a79b692b4e9c183'
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'b6de64020a5beea8add0fcf55e1389ca8404fcb0ee8bbb7260966ca2a6062c8e94c79f4d0964234fb6fe379b26fa15b426d51e59fd724560b0f954b2072e7106')
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prepare() {
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# fix snapshot tests
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patch -Np1 -i fix-tests.patch
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}
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build() {
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mkdir build
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R CMD INSTALL -l build "$_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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}
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