r-reactomegsa: fix depends, use metadata checks

BioArchLinux/r-reactomegsa/PKGBUILD

@@ -1,16 +1,16 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ReactomeGSA
-_pkgver=1.16.1
+_pkgver=1.18.0
 pkgname=r-${_pkgname,,}
-pkgver=1.16.1
-pkgrel=2
-pkgdesc='Client for the Reactome Analysis Service for comparative multi-omics gene set analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Client for the Reactome Analysis Service for comparative multi-omics gene set analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
+  r-biobase
   r-dplyr
   r-ggplot2
   r-gplots
@@ -21,27 +21,25 @@ depends=(
   r-tidyr
 )
 optdepends=(
-  r-biobase
   r-devtools
-  r-edger
   r-knitr
-  r-limma
   r-reactomegsa.data
   r-rmarkdown
-  r-scater
-  r-seurat
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('faa9aad8c282a09909833ddcc261f502f1f786869e3425626771160881b9e35c')
+md5sums=('d26ef99a4e66f2bd8260f740756ff143')
+b2sums=('a8538e564bd3b83ed1aa968f8937a6797815474a76054978bec800e4fa1b2d3cc1ec933fdfb03062256deb9ed4e82a83430e05550e9262487234fbb02b566c70')
 
 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}" "${pkgdir}/usr/lib/R/library"
-  install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-reactomegsa/lilac.py

@@ -1,12 +1,13 @@
 #!/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)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-reactomegsa/lilac.yaml

@@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-biobase
 - r-dplyr
 - r-ggplot2
 - r-gplots
@@ -12,7 +13,8 @@ repo_depends:
 - r-rcolorbrewer
 - r-tidyr
 update_on:
-- regex: ReactomeGSA_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ReactomeGSA
+- source: rpkgs
+  pkgname: ReactomeGSA
+  repo: bioc
+  md5: true
 - alias: r