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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=signifinder
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Implementations of transcriptional cancer signatures"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('AGPL-3.0-only')
depends=(
r-annotationdbi
r-biocgenerics
r-complexheatmap
r-consensusov
r-cowplot
r-dgeobj.utils
r-dplyr
r-ensembldb
r-ggplot2
r-ggridges
r-gsva
r-iranges
r-magrittr
r-matrixstats
r-maxstat
r-openair
r-org.hs.eg.db
r-patchwork
r-rcolorbrewer
r-spatialexperiment
r-summarizedexperiment
r-survminer
r-txdb.hsapiens.ucsc.hg19.knowngene
r-txdb.hsapiens.ucsc.hg38.knowngene
r-viridis
)
checkdepends=(
r-edger
r-testthat
)
optdepends=(
r-biocstyle
r-edger
r-kableextra
r-knitr
r-limma
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('f24a46dbbbc9b688450e9f2a0e2e221e')
b2sums=('fba1b218166a5dcfe58b773bceab2f987eb8db9fd70197767decc5b8120954e1277f5c5aed25b775174cce214cc878d3428fa3b44ae9d6452773690a5c8fd07a')
build() {
mkdir build
R CMD INSTALL -l build "$_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"
}
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