diff --git a/BioArchLinux/r-concordexr/PKGBUILD b/BioArchLinux/r-concordexr/PKGBUILD new file mode 100644 index 0000000000..43e0c1359c --- /dev/null +++ b/BioArchLinux/r-concordexr/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Pekka Ristola + +_pkgname=concordexR +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Calculate the concordex coefficient" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(Artistic2.0) +depends=( + r-biocparallel + r-cli + r-delayedarray + r-ggplot2 + r-pheatmap + r-rlang + r-scales +) +checkdepends=( + r-biocneighbors + r-testthat + r-vdiffr +) +optdepends=( + r-biocneighbors + r-biocstyle + r-bluster + r-covr + r-knitr + r-patchwork + r-rmarkdown + r-scater + r-tenxpbmcdata + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('8a83636d355e3b226da6f6030c17d84d') +sha256sums=('e3861fa72681a698376dc5555860a81fab3047fd64b7fc659ac5d3f5d850bcd8') + +build() { + mkdir -p build + R CMD INSTALL "$_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" +} diff --git a/BioArchLinux/r-concordexr/lilac.py b/BioArchLinux/r-concordexr/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-concordexr/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-concordexr/lilac.yaml b/BioArchLinux/r-concordexr/lilac.yaml new file mode 100644 index 0000000000..e0f7aac749 --- /dev/null +++ b/BioArchLinux/r-concordexr/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biocparallel +- r-cli +- r-delayedarray +- r-ggplot2 +- r-pheatmap +- r-rlang +- r-scales +repo_makedepends: +- r-biocneighbors +- r-testthat +- r-vdiffr +update_on: +- source: rpkgs + pkgname: concordexR + repo: bioc + md5: true +- alias: r