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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=Maaslin2
_pkgver=1.18.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="\"Multivariable Association Discovery in Population-scale Meta-omics Studies\""
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-biglm
r-car
r-chemometrics
r-cplm
r-data.table
r-dplyr
r-edger
r-ggplot2
r-glmmtmb
r-hash
r-lme4
r-lmertest
r-logging
r-metagenomeseq
r-optparse
r-pbapply
r-pcapp
r-pheatmap
r-pscl
r-robustbase
r-tibble
r-vegan
)
checkdepends=(
r-testthat
)
optdepends=(
r-knitr
r-markdown
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('65689f289ef30a89d727f676e645719a')
b2sums=('604e3069848b1a2354087b136103493095cb4a38e48ae517914054e7356b359f8ba6c5a53459e0491ff71cf13475a95db9f86080ab82ed1c5c81d03c1810c0fc')
build() {
mkdir build
R CMD INSTALL -l build "$_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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