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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=SpliceWiz
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="interactive analysis and visualization of alternative splicing in R"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-annotationhub
r-biocfilecache
r-biocgenerics
r-biocparallel
r-biostrings
r-bsgenome
r-data.table
r-delayedarray
r-delayedmatrixstats
r-dt
r-fst
r-genefilter
r-genomeinfodb
r-genomicranges
r-ggplot2
r-hdf5array
r-heatmaply
r-htmltools
r-iranges
r-magrittr
r-matrixstats
r-nxtirfdata
r-ompbam
r-patchwork
r-pheatmap
r-plotly
r-progress
r-r.utils
r-rcolorbrewer
r-rcpp
r-rhandsontable
r-rhdf5
r-rtracklayer
r-rvest
r-s4vectors
r-scales
r-shiny
r-shinydashboard
r-shinyfiles
r-shinywidgets
r-stringi
r-summarizedexperiment
zlib
)
makedepends=(
r-rcppprogress
r-zlibbioc
)
checkdepends=(
r-rsubread
r-testthat
)
optdepends=(
r-annotationdbi
r-crayon
r-dbi
r-deseq2
r-doubleexpseq
r-edger
r-fgsea
r-go.db
r-knitr
r-limma
r-rmarkdown
r-rsubread
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"link-zlib.patch")
md5sums=('2040c299f3714617473d6e1d86b79e30'
'6d95a56e1b05ba50e118ddbbee00f1cf')
b2sums=('ab9fce493d2bd7585c72c4f8eef428f880286c1a8ce541a039effc1f32c905413432badc54777d75c6a81ec37e38a21dda2245fe8e618470a2af7f87e5b5338f'
'c81190033eaba3e11043f9eb9ab2e0275b37a40ba6d5ad821a37560c74f3dc65a0fe3e0e9c4825fcc23e6bd9a7084ff0ba144daa6ef7b564517e4af2b4471362')
prepare() {
cd "$_pkgname"
# link to zlib
patch -Np1 -i ../link-zlib.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"
install -d "$pkgdir/usr/share/licenses/$pkgname"
ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
}
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