diff --git a/BioArchLinux/r-cancer/PKGBUILD b/BioArchLinux/r-cancer/PKGBUILD index 32a2c936a9..3eac20a11c 100644 --- a/BioArchLinux/r-cancer/PKGBUILD +++ b/BioArchLinux/r-cancer/PKGBUILD @@ -1,22 +1,21 @@ # Maintainer: Guoyi Zhang _pkgname=canceR -_pkgver=1.36.0 +_pkgver=1.36.2 pkgname=r-${_pkgname,,} -pkgver=1.36.0 -pkgrel=1 -pkgdesc='A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgver=${_pkgver//-/.} +pkgrel=0 +pkgdesc="A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-only') depends=( - r r-biobase + r-cbioportaldata r-circlize r-formula r-genetclassifier r-gseabase - r-httr r-phenotest r-plyr r-r.methodss3 @@ -31,14 +30,15 @@ optdepends=( r-testthat ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('8bd3f06dde9650dec31739a7d719c05eba741242add438dba8df6f4088f65c53') +md5sums=('7d3c7532e79982ee5db6e3aa3788381e') +b2sums=('1684e18f87b95f7650924a48df3c2263d3ab7f610b5718d3d8429311b08ca50cb87044cb837e34bf6269e377aaf1d93c50aebd4b72118385601681c9a72f1b13') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-cancer/lilac.py b/BioArchLinux/r-cancer/lilac.py index bd219c037c..11d9093b39 100644 --- a/BioArchLinux/r-cancer/lilac.py +++ b/BioArchLinux/r-cancer/lilac.py @@ -1,12 +1,16 @@ #!/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(): - 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('-', '.')) + r_pre_build( + _G, + expect_systemrequirements = "Tktable, BWidget", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-cancer/lilac.yaml b/BioArchLinux/r-cancer/lilac.yaml index 7777beb9f8..bd373a4bbf 100644 --- a/BioArchLinux/r-cancer/lilac.yaml +++ b/BioArchLinux/r-cancer/lilac.yaml @@ -4,11 +4,11 @@ maintainers: email: kuoi@bioarchlinux.org repo_depends: - r-biobase +- r-cbioportaldata - r-circlize - r-formula - r-genetclassifier - r-gseabase -- r-httr - r-phenotest - r-plyr - r-r.methodss3 @@ -16,8 +16,8 @@ repo_depends: - r-runit - r-tkrplot update_on: -- regex: canceR_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/canceR +- source: rpkgs + pkgname: canceR + repo: bioc + md5: true - alias: r -time_limit_hours: 6