r-multirnaflow: init

BioArchLinux/r-multirnaflow/PKGBUILD

@@ -0,0 +1,63 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_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"
+}

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()

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

BioArchLinux/r-plot3drgl/PKGBUILD

@@ -0,0 +1,30 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Robert Greener <me@r0bert.dev>
+# 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"
+}

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()

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

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",