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r-syntenet: init, dependency of r-doubletrouble
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65
BioArchLinux/r-syntenet/PKGBUILD
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65
BioArchLinux/r-syntenet/PKGBUILD
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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
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_pkgname=syntenet
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_pkgver=1.2.4
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pkgname=r-${_pkgname,,}
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pkgver=${_pkgver//-/.}
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pkgrel=1
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pkgdesc="Inference And Analysis Of Synteny Networks"
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arch=(x86_64)
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url="https://bioconductor.org/packages/${_pkgname}"
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license=(GPL3)
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depends=(
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r-biocparallel
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r-biostrings
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r-genomicranges
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r-ggnetwork
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r-ggplot2
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r-igraph
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r-intergraph
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r-networkd3
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r-pheatmap
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r-rcolorbrewer
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r-rcpp
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r-rlang
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r-rtracklayer
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)
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makedepends=(
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r-testthat
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)
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checkdepends=(
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r-xml2
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)
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optdepends=(
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r-biocstyle
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r-covr
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r-ggtree
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r-knitr
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r-labdsv
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r-rmarkdown
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r-testthat
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r-xml2
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
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md5sums=('81bd02bbba83fcb7f62098b5fd2a1fc6')
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sha256sums=('d5cb3ad5a92be38fa9a538dc856002464d4d353400d126f6840ed4e3bd74a02e')
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prepare() {
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# skip tests that cause a coredump
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sed -i '1i skip("dumps core")' "$_pkgname/tests/testthat/test-03_synteny_detection.R"
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}
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build() {
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mkdir -p build
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R CMD INSTALL "$_pkgname" -l build
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}
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check() {
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cd "$_pkgname/tests"
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R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
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}
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package() {
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install -d "$pkgdir/usr/lib/R/library"
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cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
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}
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14
BioArchLinux/r-syntenet/lilac.py
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BioArchLinux/r-syntenet/lilac.py
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#!/usr/bin/env python3
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from lilaclib import *
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import os
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import sys
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sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
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from lilac_r_utils import r_pre_build
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def pre_build():
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r_pre_build(_G)
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def post_build():
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git_pkgbuild_commit()
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update_aur_repo()
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27
BioArchLinux/r-syntenet/lilac.yaml
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27
BioArchLinux/r-syntenet/lilac.yaml
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build_prefix: extra-x86_64
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maintainers:
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- github: pekkarr
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email: pekkarr@protonmail.com
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repo_depends:
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- r-biocparallel
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- r-biostrings
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- r-genomicranges
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- r-ggnetwork
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- r-ggplot2
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- r-igraph
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- r-intergraph
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- r-networkd3
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- r-pheatmap
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- r-rcolorbrewer
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- r-rcpp
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- r-rlang
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- r-rtracklayer
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repo_makedepends:
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- r-testthat
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- r-xml2
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update_on:
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- source: rpkgs
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pkgname: syntenet
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repo: bioc
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md5: true
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- alias: r
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