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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=epimutacions
_pkgver=1.10.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Robust outlier identification for DNA methylation data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('MIT')
depends=(
r-annotationdbi
r-annotationhub
r-biocgenerics
r-biocparallel
r-biomart
r-bumphunter
r-ensembldb
r-epimutacionsdata
r-experimenthub
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-ggplot2
r-ggrepel
r-gridextra
r-gviz
r-homo.sapiens
r-illuminahumanmethylation450kanno.ilmn12.hg19
r-illuminahumanmethylation450kmanifest
r-illuminahumanmethylationepicanno.ilm10b2.hg19
r-illuminahumanmethylationepicmanifest
r-iranges
r-isotree
r-matrixstats
r-minfi
r-purrr
r-reshape2
r-robustbase
r-rtracklayer
r-s4vectors
r-summarizedexperiment
r-tibble
r-txdb.hsapiens.ucsc.hg18.knowngene
r-txdb.hsapiens.ucsc.hg19.knowngene
r-txdb.hsapiens.ucsc.hg38.knowngene
)
checkdepends=(
r-testthat
)
optdepends=(
r-a4base
r-biocstyle
r-kableextra
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('30df10a44d353e8f963c72c0822682e3')
b2sums=('b6bdb467e04f9db2731ef035c25c817c05fe20ff5a8eb21f97bc4cd2a98f9ffaf34f8c0f7fd196e08673d68ae0b1280d7eaff4dc3c2454cf3a251e1d8745e530')
build() {
mkdir build
R CMD INSTALL -l build "$_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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