r-cancer: fix depends, use metadata checks

BioArchLinux/r-cancer/PKGBUILD

@@ -1,22 +1,21 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=canceR
-_pkgver=1.36.0
+_pkgver=1.36.2
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
+pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=0
-pkgdesc='A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC'
+pkgdesc="A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('GPL')
+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 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

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'):
+    r_pre_build(
-        if line.startswith('_pkgver='):
+        _G,
-            line = f'_pkgver={_G.newver}'
+        expect_systemrequirements = "Tktable, BWidget",
-        print(line)
+    )
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

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: rpkgs
-  source: regex
+  pkgname: canceR
-  url: https://bioconductor.org/packages/canceR
+  repo: bioc
+  md5: true
 - alias: r
-time_limit_hours: 6