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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=Maaslin2
_pkgver=1.22.0
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}_${_pkgver}.tar.gz")
md5sums=('7f5c262861a87a22260455344dee7f44')
b2sums=('68439a99d5822842efbed371da839cddea9e0163361e85dd7f4039011e4c27f98de7cef78d423525a435e664797e9f89333cb49aba58b70925979dd5b89711a9')
build() {
mkdir build
R CMD INSTALL -l build "$_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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