r-stdeconvolve: init

BioArchLinux/r-liger/PKGBUILD

@@ -0,0 +1,36 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=liger
+_pkgver=2.0.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Lightweight Iterative Geneset Enrichment"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-matrixstats
+  r-rcpp
+)
+makedepends=(
+  r-rcpparmadillo
+)
+optdepends=(
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d7a410589d361d183968613aeed4fd2a')
+sha256sums=('c1eb36962ed679b82811af9568dfae96a85dd000a2750a61171d906a3fbf3188')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-liger/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-liger/lilac.yaml

@@ -0,0 +1,15 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-matrixstats
+- r-rcpp
+repo_makedepends:
+- r-rcpparmadillo
+update_on:
+- source: rpkgs
+  pkgname: liger
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-stdeconvolve/PKGBUILD

@@ -0,0 +1,54 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=STdeconvolve
+_pkgver=1.6.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-biocparallel
+  r-clue
+  r-ggplot2
+  r-liger
+  r-reshape2
+  r-scatterpie
+  r-slam
+  r-topicmodels
+  r-viridis
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-dplyr
+  r-gplots
+  r-gridextra
+  r-hash
+  r-knitr
+  r-rcmdcheck
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('2908e0d59713b2c3ef6c7bc549d0d123')
+sha256sums=('172c5e0ed57d279eaebc7496e7be51af4d460aa2902495abbc5a6aee91077c9b')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-stdeconvolve/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-stdeconvolve/lilac.yaml

@@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocparallel
+- r-clue
+- r-ggplot2
+- r-liger
+- r-reshape2
+- r-scatterpie
+- r-slam
+- r-topicmodels
+- r-viridis
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: STdeconvolve
+  repo: bioc
+  md5: true
+- alias: r