diff --git a/fail/r-affypara/PKGBUILD b/BioArchLinux/r-affypara/PKGBUILD similarity index 53% rename from fail/r-affypara/PKGBUILD rename to BioArchLinux/r-affypara/PKGBUILD index 9d2cc41c3e..31fe38e36e 100644 --- a/fail/r-affypara/PKGBUILD +++ b/BioArchLinux/r-affypara/PKGBUILD @@ -1,13 +1,13 @@ _pkgname=affyPara -_pkgver=1.34.0 +_pkgver=1.54.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//[:-]/.} pkgrel=1 pkgdesc='Sample size for RNAseq studies' arch=('any') url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +license=('GPL3') depends=( r r-affy @@ -27,6 +27,18 @@ optdepends=( source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") sha256sums=('SKIP') +prepare(){ + # remove 22c `assign(".affyParaInternalEnv", .affyParaInternalEnv, envir=topenv(parent.frame()))` + # adapted from + # https://github.com/tidyverse/ggplot2/blob/7ebb6bd9d664f58794078afdb5a8ff71d5edf96d/R/ggplot-global.R#L4 + sed -i '/assign(".affyParaInternalEnv/d' ${_pkgname}/R/zzz.R + + # mv .affyParaInternalEnv <- new.env(parent=emptyenv()) to top of the file. + grep -E '^\s+.affyParaInternalEnv' ${_pkgname}/R/zzz.R > tmpzzz.R + grep -vE '^\s+.affyParaInternalEnv' ${_pkgname}/R/zzz.R >> tmpzzz.R + mv tmpzzz.R ${_pkgname}/R/zzz.R +} + build() { tar -zcvf ${_pkgname}.tar.gz ${_pkgname} R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" diff --git a/fail/r-affypara/lilac.py b/BioArchLinux/r-affypara/lilac.py similarity index 100% rename from fail/r-affypara/lilac.py rename to BioArchLinux/r-affypara/lilac.py diff --git a/fail/r-affypara/lilac.yaml b/BioArchLinux/r-affypara/lilac.yaml similarity index 77% rename from fail/r-affypara/lilac.yaml rename to BioArchLinux/r-affypara/lilac.yaml index 7fa4ef63e8..045f8b919e 100644 --- a/fail/r-affypara/lilac.yaml +++ b/BioArchLinux/r-affypara/lilac.yaml @@ -11,4 +11,4 @@ repo_depends: update_on: - regex: (\d+.\d+.\d+) source: regex - url: https://bioconductor.org/packages/affyPara + url: https://bioconductor.org/packages/3.14/bioc/html/affyPara.html diff --git a/BioArchLinux/r-hgu95av2cdf/PKGBUILD b/BioArchLinux/r-hgu95av2cdf/PKGBUILD new file mode 100644 index 0000000000..5c8a9a30e6 --- /dev/null +++ b/BioArchLinux/r-hgu95av2cdf/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: sukanka + +_pkgname=hgu95av2cdf +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='hgu95av2cdf' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('d449a06a2f55a5a1f942710c8da2a37a81e20342b6e600669df94ecb55f1e1fe') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-hgu95av2cdf/lilac.py b/BioArchLinux/r-hgu95av2cdf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/BioArchLinux/r-hgu95av2cdf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/BioArchLinux/r-hgu95av2cdf/lilac.yaml b/BioArchLinux/r-hgu95av2cdf/lilac.yaml new file mode 100644 index 0000000000..e60d9a6b93 --- /dev/null +++ b/BioArchLinux/r-hgu95av2cdf/lilac.yaml @@ -0,0 +1,9 @@ +build_prefix: extra-x86_64 +maintainers: + - github: sukanka +repo_depends: + - r-annotationdbi +update_on: + - regex: hgu95av2cdf_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hgu95av2cdf