r-limma: fix depends, use metadata checks

BioArchLinux/r-limma/PKGBUILD

@@ -1,42 +1,43 @@
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=limma
-_pkgver=3.56.2
+_pkgver=3.58.0
 pkgname=r-${_pkgname,,}
-pkgver=3.56.2
-pkgrel=1
-pkgdesc='Linear Models for Microarray Data'
-arch=('x86_64')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Linear Models for Microarray Data"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+license=(GPL)
 depends=(
-  r
+  r-statmod
 )
 optdepends=(
   r-affy
   r-annotationdbi
   r-biasedurn
   r-biobase
+  r-biocstyle
   r-ellipse
   r-go.db
   r-gplots
   r-illuminaio
+  r-knitr
   r-locfit
-  r-mass
   r-org.hs.eg.db
-  r-splines
-  r-statmod
   r-vsn
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('19d8090708a38d7320e797df27455e60eaafdc02f97ecae62537d8ec925a3e56')
+md5sums=('521e5f19c19affa0ead9e097967701e8')
+sha256sums=('ee4510e8208e564dc5d32c2ba58741b6a3c155e9b90c5fe4a299e98886f71fd6')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
 }
 
 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:

BioArchLinux/r-limma/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_license = "GPL (>=2)",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-limma/lilac.yaml

@@ -1,9 +1,12 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-statmod
 update_on:
-- regex: limma_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/limma
+- source: rpkgs
+  pkgname: limma
+  repo: bioc
+  md5: true
 - alias: r