r-factr: init

BioArchLinux/r-factr/PKGBUILD

@@ -0,0 +1,75 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=factR
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Functional Annotation of Custom Transcriptomes"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Apache)
+depends=(
+  r-biocgenerics
+  r-biocparallel
+  r-biostrings
+  r-crayon
+  r-data.table
+  r-dplyr
+  r-drawproteins
+  r-genomeinfodb
+  r-genomicfeatures
+  r-genomicranges
+  r-ggplot2
+  r-iranges
+  r-pbapply
+  r-purrr
+  r-rcurl
+  r-rlang
+  r-rtracklayer
+  r-s4vectors
+  r-stringr
+  r-tibble
+  r-tidyr
+  r-wiggleplotr
+  r-xml
+)
+checkdepends=(
+  r-annotationhub
+  r-bsgenome.mmusculus.ucsc.mm10
+  r-testthat
+)
+optdepends=(
+  r-annotationhub
+  r-bio3d
+  r-bsgenome
+  r-bsgenome.mmusculus.ucsc.mm10
+  r-covr
+  r-knitr
+  r-markdown
+  r-patchwork
+  r-rmarkdown
+  r-rmdformats
+  r-signalhsmm
+  r-testthat
+  r-tidyverse
+  r-zeallot
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('55b088d84e382a7068b40062151e4bec')
+sha256sums=('bb37f5dfd3ff46d37ff4ae979b5cb6753d953372522fac7e740f3869313e99e4')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-factr/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 = "file LICENSE",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-factr/lilac.yaml

@@ -0,0 +1,38 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocgenerics
+- r-biocparallel
+- r-biostrings
+- r-crayon
+- r-data.table
+- r-dplyr
+- r-drawproteins
+- r-genomeinfodb
+- r-genomicfeatures
+- r-genomicranges
+- r-ggplot2
+- r-iranges
+- r-pbapply
+- r-purrr
+- r-rcurl
+- r-rlang
+- r-rtracklayer
+- r-s4vectors
+- r-stringr
+- r-tibble
+- r-tidyr
+- r-wiggleplotr
+- r-xml
+repo_makedepends:
+- r-annotationhub
+- r-bsgenome.mmusculus.ucsc.mm10
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: factR
+  repo: bioc
+  md5: true
+- alias: r