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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=benchdamic
_pkgver=1.8.2
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Benchmark of differential abundance methods on microbiome data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-aldex2
r-ancombc
r-biocparallel
r-cowplot
r-dearseq
r-deseq2
r-edger
r-ggdendro
r-ggplot2
r-ggridges
r-gunifrac
r-limma
r-lme4
r-maaslin2
r-mast
r-metagenomeseq
r-mglm
r-microbiomestat
r-mixomics
r-noiseq
r-phyloseq
r-plyr
r-rcolorbrewer
r-reshape2
r-seurat
r-summarizedexperiment
r-tidytext
r-treesummarizedexperiment
r-zinbwave
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-kableextra
r-knitr
r-magick
r-rmarkdown
r-spsimseq
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('3e181e9df4a701c33b61a184a26f0a59')
b2sums=('1588d6de023a6f80582bdffc8de610b0830ac1a0120e4ed3018b585082a55018b3f4b17df7cd02289033ea30f565dc085a6445fb8b6d78daf314f8c03488f309')
build() {
mkdir build
R CMD INSTALL -l build "$_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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