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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=benchdamic
_pkgver=1.10.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Benchmark of differential abundance methods on microbiome data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-aldex2
r-ancombc
r-biocparallel
r-corncob
r-cowplot
r-dearseq
r-deseq2
r-edger
r-ggdendro
r-ggplot2
r-ggridges
r-gunifrac
r-limma
r-lme4
r-maaslin2
r-mast
r-metagenomeseq
r-mglm
r-microbiomestat
r-mixomics
r-noiseq
r-phyloseq
r-plyr
r-rcolorbrewer
r-reshape2
r-seurat
r-summarizedexperiment
r-tidytext
r-treesummarizedexperiment
r-zinbwave
)
checkdepends=(
r-testthat
)
optdepends=(
r-biocstyle
r-kableextra
r-knitr
r-magick
r-rmarkdown
r-spsimseq
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('da159f53d1021bd6dc0e48daa53e40b0')
b2sums=('95ee6b07483ebde2d27d2a43cb63c270693275e994a7f76dc700e6881fb0767f33ecdf357afc5cd963631e933208115027723d8297d6e709bd8f21109f720da5')
build() {
mkdir build
R CMD INSTALL -l build "$_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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