r-extrachips: init

BioArchLinux/r-extrachips/PKGBUILD

@@ -0,0 +1,85 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=extraChIPs
+_pkgver=1.6.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Additional functions for working with ChIP-Seq data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-biocio
+  r-biocparallel
+  r-broom
+  r-complexupset
+  r-csaw
+  r-dplyr
+  r-edger
+  r-enrichedheatmap
+  r-forcats
+  r-genomeinfodb
+  r-genomicinteractions
+  r-genomicranges
+  r-ggforce
+  r-ggplot2
+  r-ggrepel
+  r-ggside
+  r-glue
+  r-gviz
+  r-interactionset
+  r-iranges
+  r-limma
+  r-matrixstats
+  r-patchwork
+  r-rcolorbrewer
+  r-rlang
+  r-rsamtools
+  r-rtracklayer
+  r-s4vectors
+  r-scales
+  r-stringr
+  r-summarizedexperiment
+  r-tibble
+  r-tidyr
+  r-tidyselect
+  r-vctrs
+  r-venndiagram
+)
+checkdepends=(
+  r-harmonicmeanp
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-covr
+  r-cqn
+  r-harmonicmeanp
+  r-here
+  r-knitr
+  r-magrittr
+  r-plyranges
+  r-quantro
+  r-rmarkdown
+  r-testthat
+  r-tidyverse
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('462672c12f16f912b7e3d4b30a07162f')
+sha256sums=('92031cff96880e0e7c1cfa46084ec580991c01a7e23c0734f1802778a1e0c47e')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-extrachips/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-extrachips/lilac.yaml

@@ -0,0 +1,50 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocio
+- r-biocparallel
+- r-broom
+- r-complexupset
+- r-csaw
+- r-dplyr
+- r-edger
+- r-enrichedheatmap
+- r-forcats
+- r-genomeinfodb
+- r-genomicinteractions
+- r-genomicranges
+- r-ggforce
+- r-ggplot2
+- r-ggrepel
+- r-ggside
+- r-glue
+- r-gviz
+- r-interactionset
+- r-iranges
+- r-limma
+- r-matrixstats
+- r-patchwork
+- r-rcolorbrewer
+- r-rlang
+- r-rsamtools
+- r-rtracklayer
+- r-s4vectors
+- r-scales
+- r-stringr
+- r-summarizedexperiment
+- r-tibble
+- r-tidyr
+- r-tidyselect
+- r-vctrs
+- r-venndiagram
+repo_makedepends:
+- r-harmonicmeanp
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: extraChIPs
+  repo: bioc
+  md5: true
+- alias: r