r-orthos: init

BioArchLinux/r-orthos/PKGBUILD

@@ -0,0 +1,59 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=orthos
+_pkgver=1.0.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="\`orthos\` is an R package for variance decomposition using conditional variational auto-encoders"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-annotationhub
+  r-basilisk
+  r-biocparallel
+  r-colorspace
+  r-cowplot
+  r-delayedarray
+  r-dplyr
+  r-experimenthub
+  r-ggplot2
+  r-ggpubr
+  r-ggrepel
+  r-ggsci
+  r-hdf5array
+  r-keras
+  r-orthosdata
+  r-plyr
+  r-reticulate
+  r-rlang
+  r-s4vectors
+  r-summarizedexperiment
+  r-tensorflow
+  r-tidyr
+)
+optdepends=(
+  r-biocmanager
+  r-biocstyle
+  r-htmltools
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('c35d515c0e956e4207b00db662192707')
+sha256sums=('8b7b30496fe70f7dd55c55a87894b01003cc1628100ed0de5f8b71bdaaa62b6a')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-orthos/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-orthos/lilac.yaml

@@ -0,0 +1,33 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-annotationhub
+- r-basilisk
+- r-biocparallel
+- r-colorspace
+- r-cowplot
+- r-delayedarray
+- r-dplyr
+- r-experimenthub
+- r-ggplot2
+- r-ggpubr
+- r-ggrepel
+- r-ggsci
+- r-hdf5array
+- r-keras
+- r-orthosdata
+- r-plyr
+- r-reticulate
+- r-rlang
+- r-s4vectors
+- r-summarizedexperiment
+- r-tensorflow
+- r-tidyr
+update_on:
+- source: rpkgs
+  pkgname: orthos
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-orthosdata/PKGBUILD

@@ -0,0 +1,42 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=orthosData
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Data for the orthos package"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-annotationhub
+  r-biocfilecache
+  r-experimenthub
+  r-hdf5array
+  r-stringr
+  r-summarizedexperiment
+)
+optdepends=(
+  r-biocstyle
+  r-ggplot2
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('7970587455fa5197daf1f6b640b7f688')
+sha256sums=('631be84ad27eea65697c93a491fa96afcde226e05876cb9d644940d5dd9e3b59')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-orthosdata/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-orthosdata/lilac.yaml

@@ -0,0 +1,17 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-annotationhub
+- r-biocfilecache
+- r-experimenthub
+- r-hdf5array
+- r-stringr
+- r-summarizedexperiment
+update_on:
+- source: rpkgs
+  pkgname: orthosData
+  repo: bioc-data-experiment
+  md5: true
+- alias: r

lilac-extensions/lilac_r_utils.py

@@ -181,7 +181,7 @@ class Pkgbuild:
     def _parse_value(self, value: str) -> str:
         if value[0] != '"' or value[-1] != '"':
             raise Exception("Fatal error")
-        return value[1:-1].replace('\\"', '"').replace('\\\\', '\\')
+        return value[1:-1].replace('\\$', '$').replace('\\`', '`').replace('\\"', '"').replace('\\\\', '\\')
 
 # maps the license field in the DESCRIPTION file to a PKGBUILD license value
 license_map = {