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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=EpiMix
_pkgver=1.6.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="an integrative tool for the population-level analysis of DNA methylation"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-annotationdbi
r-annotationhub
r-biobase
r-biomart
r-data.table
r-doparallel
r-dosnow
r-downloader
r-dplyr
r-elmer.data
r-epimix.data
r-experimenthub
r-foreach
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-ggplot2
r-impute
r-iranges
r-limma
r-plyr
r-progress
r-r.matlab
r-rcolorbrewer
r-rcurl
r-rlang
r-rpmm
r-s4vectors
r-summarizedexperiment
r-tibble
r-tidyr
)
checkdepends=(
r-biocgenerics
r-runit
r-sesamedata
)
optdepends=(
r-biocgenerics
r-biocstyle
r-clusterprofiler
r-dt
r-geoquery
r-karyoploter
r-knitr
r-mirbaseconverter
r-multimir
r-org.hs.eg.db
r-regioner
r-runit
r-seurat
r-survminer
r-txdb.hsapiens.ucsc.hg19.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('eabf88cbeaf4f32228191f3a389c880a')
b2sums=('d1c3f93e97ecc9a568cf57d47961fc89c43eaf577801275efd50ee1082711647bc637b9e8fb522abc918d9e747052dcffbeab87b756af3430df451b89d9364b3')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
check() {
cd "$_pkgname/tests"
R_LIBS="$srcdir/build" Rscript --vanilla runTests.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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