r-fgsea: use metadata checks

BioArchLinux/r-fgsea/PKGBUILD

@@ -1,19 +1,16 @@
-# system requirements: C++11
-# 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=fgsea
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
-pkgver=1.26.0
+pkgver=${_pkgver//-/.}
 pkgrel=3
-pkgdesc='Fast Gene Set Enrichment Analysis'
-arch=('x86_64')
+pkgdesc="Fast Gene Set Enrichment Analysis"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('MIT')
+license=(MIT)
 depends=(
-  gcc
-  r
-  r-bh
   r-biocparallel
   r-cowplot
   r-data.table
@@ -22,6 +19,15 @@ depends=(
   r-rcpp
   r-scales
 )
+makedepends=(
+  r-bh
+)
+checkdepends=(
+  r-geoquery
+  r-limma
+  r-reactome.db
+  r-testthat
+)
 optdepends=(
   r-aggregation
   r-annotationdbi
@@ -30,22 +36,29 @@ optdepends=(
   r-limma
   r-msigdbr
   r-org.mm.eg.db
-  r-parallel
   r-reactome.db
   r-rmarkdown
   r-seurat
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3b02276027800535421f38bbe5e83921')
 sha256sums=('ffd44dcf4e4a757ae4c79f3df99897a3e126fbca3e54457ace2c8cc923cf1632')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
-  install -Dm644 "${_pkgname}/LICENCE" -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/LICENCE" "$pkgdir/usr/share/licenses/$pkgname"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-fgsea/lilac.py

@@ -1,12 +1,17 @@
 #!/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 = "MIT + file LICENCE",
+        expect_systemrequirements = "C++11",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-fgsea/lilac.yaml

@@ -1,9 +1,8 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
-- r-bh
 - r-biocparallel
 - r-cowplot
 - r-data.table
@@ -11,8 +10,15 @@ repo_depends:
 - r-ggplot2
 - r-rcpp
 - r-scales
+repo_makedepends:
+- r-bh
+- r-geoquery
+- r-limma
+- r-reactome.db
+- r-testthat
 update_on:
-- regex: fgsea_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/fgsea
+- source: rpkgs
+  pkgname: fgsea
+  repo: bioc
+  md5: true
 - alias: r