diff --git a/BioArchLinux/r-factr/PKGBUILD b/BioArchLinux/r-factr/PKGBUILD new file mode 100644 index 0000000000..308ded9958 --- /dev/null +++ b/BioArchLinux/r-factr/PKGBUILD @@ -0,0 +1,75 @@ +# Maintainer: Pekka Ristola + +_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" +} diff --git a/BioArchLinux/r-factr/lilac.py b/BioArchLinux/r-factr/lilac.py new file mode 100644 index 0000000000..c808eaf563 --- /dev/null +++ b/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() diff --git a/BioArchLinux/r-factr/lilac.yaml b/BioArchLinux/r-factr/lilac.yaml new file mode 100644 index 0000000000..6b3d70682c --- /dev/null +++ b/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