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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=coMethDMR
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-annotationhub
r-biocparallel
r-bumphunter
r-experimenthub
r-genomicranges
r-iranges
r-lmertest
)
checkdepends=(
r-illuminahumanmethylation450kanno.ilmn12.hg19
r-sesamedata
r-testthat
)
optdepends=(
r-biocstyle
r-corrplot
r-illuminahumanmethylation450kanno.ilmn12.hg19
r-illuminahumanmethylationepicanno.ilm10b4.hg19
r-knitr
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('0a6229d90868a4a60eb0f72c4499d1fc')
b2sums=('b43b978f0621e85d47af43f9c06ff3f94e5f20a71f7866adc8852e30d8adf275926df630485a3f4a21c0f538cab8c9fd8186f3431e063e12ac503fb4510bbc63')
build() {
mkdir build
R CMD INSTALL -l build "$_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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