r-geotcgadata: init

BioArchLinux/r-geotcgadata/PKGBUILD

@@ -0,0 +1,67 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=GeoTcgaData
+_pkgver=2.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Processing Various Types of Data on GEO and TCGA"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-cqn
+  r-data.table
+  r-plyr
+  r-summarizedexperiment
+  r-topconfects
+)
+checkdepends=(
+  r-clusterprofiler
+  r-edger
+  r-limma
+  r-org.hs.eg.db
+  r-testthat
+)
+optdepends=(
+  r-biocgenerics
+  r-catt
+  r-champ
+  r-clusterprofiler
+  r-dearseq
+  r-deseq2
+  r-edger
+  r-enrichplot
+  r-geoquery
+  r-illuminahumanmethylation450kanno.ilmn12.hg19
+  r-impute
+  r-knitr
+  r-limma
+  r-minfi
+  r-noiseq
+  r-org.hs.eg.db
+  r-quantreg
+  r-rmarkdown
+  r-s4vectors
+  r-tcgabiolinks
+  r-testthat
+  r-tidyr
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('463ef0f64e092337495a3f6da55b224a')
+sha256sums=('314062425c9e61fc002de591495c9fa57821fe8163c0e41542d7d0c14f4d6f39')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-geotcgadata/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-geotcgadata/lilac.yaml

@@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-cqn
+- r-data.table
+- r-plyr
+- r-summarizedexperiment
+- r-topconfects
+repo_makedepends:
+- r-clusterprofiler
+- r-edger
+- r-limma
+- r-org.hs.eg.db
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: GeoTcgaData
+  repo: bioc
+  md5: true
+- alias: r