diff --git a/BioArchLinux/r-multirnaflow/PKGBUILD b/BioArchLinux/r-multirnaflow/PKGBUILD new file mode 100644 index 0000000000..1735da26af --- /dev/null +++ b/BioArchLinux/r-multirnaflow/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Pekka Ristola + +_pkgname=MultiRNAflow +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="An R package for analysing RNA-seq raw counts with several biological conditions and different time points" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(GPL3) +depends=( + r-biobase + r-complexheatmap + r-deseq2 + r-factoextra + r-factominer + r-ggalluvial + r-ggplot2 + r-ggrepel + r-ggsci + r-gprofiler2 + r-mfuzz + r-plot3d + r-plot3drgl + r-plyr + r-rcolorbrewer + r-reshape2 + r-rlang + r-s4vectors + r-scales + r-summarizedexperiment + r-upsetr +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocgenerics + r-biocstyle + r-e1071 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('cefc109896f4cb34b4ee6a09ae966f42') +sha256sums=('5e7e81f1e25b61abd3f2cdee0e39527ccd0b92a2029b3d88a148d905478378ed') + +build() { + mkdir -p build + R CMD INSTALL "$_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" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-multirnaflow/lilac.py b/BioArchLinux/r-multirnaflow/lilac.py new file mode 100644 index 0000000000..b5d481821a --- /dev/null +++ b/BioArchLinux/r-multirnaflow/lilac.py @@ -0,0 +1,17 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build( + _G, + expect_license = "GPL-3 | file LICENSE", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-multirnaflow/lilac.yaml b/BioArchLinux/r-multirnaflow/lilac.yaml new file mode 100644 index 0000000000..483272e55b --- /dev/null +++ b/BioArchLinux/r-multirnaflow/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biobase +- r-complexheatmap +- r-deseq2 +- r-factoextra +- r-factominer +- r-ggalluvial +- r-ggplot2 +- r-ggrepel +- r-ggsci +- r-gprofiler2 +- r-mfuzz +- r-plot3d +- r-plot3drgl +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-rlang +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-upsetr +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: MultiRNAflow + repo: bioc + md5: true +- alias: r diff --git a/BioArchLinux/r-plot3drgl/PKGBUILD b/BioArchLinux/r-plot3drgl/PKGBUILD new file mode 100644 index 0000000000..53045ea15e --- /dev/null +++ b/BioArchLinux/r-plot3drgl/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Pekka Ristola +# Contributor: Robert Greener +# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com + +_pkgname=plot3Drgl +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=0 +pkgdesc="Plotting Multi-Dimensional Data - Using 'rgl'" +arch=(any) +url="https://cran.r-project.org/package=${_pkgname}" +license=(GPL3) +depends=( + r-plot3d + r-rgl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('4703ef94b1a0b6eed095071d280ac1e4') +sha256sums=('6d87a9a32aba3aa64f751268cabd14dbd3e0eca2bd5f0a4b11366cd1e2f51bdd') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-plot3drgl/lilac.py b/BioArchLinux/r-plot3drgl/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-plot3drgl/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-plot3drgl/lilac.yaml b/BioArchLinux/r-plot3drgl/lilac.yaml new file mode 100644 index 0000000000..de420571b1 --- /dev/null +++ b/BioArchLinux/r-plot3drgl/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-plot3d +- r-rgl +update_on: +- source: rpkgs + pkgname: plot3Drgl + repo: cran + md5: true +- alias: r diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py index d19387185f..f05b4fd39e 100644 --- a/lilac-extensions/lilac_r_utils.py +++ b/lilac-extensions/lilac_r_utils.py @@ -200,6 +200,7 @@ license_map = { "GPL (>= 2)": "GPL", "GPL (>= 2.0)": "GPL", "GPL (>= 3)": "GPL3", + "GPL (>= 3.0)": "GPL3", "GPL-2": "GPL2", "GPL-2 | GPL-3": "GPL", "GPL-3": "GPL3",