diff --git a/BioArchLinux/r-regionalpcs/PKGBUILD b/BioArchLinux/r-regionalpcs/PKGBUILD new file mode 100644 index 0000000000..5a49efdb86 --- /dev/null +++ b/BioArchLinux/r-regionalpcs/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Pekka Ristola + +_pkgname=regionalpcs +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Summarizing Regional Methylation with Regional Principal Components Analysis" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(MIT) +depends=( + r-dplyr + r-genomicranges + r-pcatools + r-tibble +) +checkdepends=( + r-rmtstat + r-testthat +) +optdepends=( + r-biocstyle + r-iranges + r-knitr + r-minfidata + r-rmarkdown + r-rmtstat + r-testthat + r-tidyr + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('37f0fc1370efacc719f72b419455096a') +sha256sums=('e16add6355dc7e8f0abf1e64ebf7d630353fbe344029064834c5504ae6e9403d') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +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" +} diff --git a/BioArchLinux/r-regionalpcs/lilac.py b/BioArchLinux/r-regionalpcs/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-regionalpcs/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-regionalpcs/lilac.yaml b/BioArchLinux/r-regionalpcs/lilac.yaml new file mode 100644 index 0000000000..11642849b1 --- /dev/null +++ b/BioArchLinux/r-regionalpcs/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-dplyr +- r-genomicranges +- r-pcatools +- r-tibble +repo_makedepends: +- r-rmtstat +- r-testthat +update_on: +- source: rpkgs + pkgname: regionalpcs + repo: bioc + md5: true +- alias: r