r-chemminer: use metadata checks

BioArchLinux/r-chemminer/PKGBUILD

@@ -1,19 +1,17 @@
-# system requirements: GNU make
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ChemmineR
 _pkgver=3.52.0
 pkgname=r-${_pkgname,,}
-pkgver=3.52.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Cheminformatics Toolkit for R'
+pkgdesc="Cheminformatics Toolkit for R"
-arch=('x86_64')
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  r
   r-base64enc
-  r-bh
   r-biocgenerics
   r-dbi
   r-digest
@@ -27,20 +25,26 @@ depends=(
   r-rjson
   r-rsvg
   r-stringi
-  make
+)
+makedepends=(
+  r-bh
+  swig
+)
+checkdepends=(
+  r-rsqlite
+  r-runit
+  r-snow
 )
 optdepends=(
   r-bibtex
   r-biocmanager
   r-biocstyle
   r-chemminedrugs
-  r-chemmineob
   r-fmcsr
   r-gplots
   r-knitcitations
   r-knitr
   r-knitrbootstrap
-  r-png
   r-rmarkdown
   r-rpostgresql
   r-rsqlite
@@ -48,14 +52,25 @@ optdepends=(
   r-snow
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('54601905e8a4a48d85b3c7a80f935eb5')
 sha256sums=('3d24d7b81d8d5315c53b5c04002b39d0f2b5354b992b66d73cca4ff0077e9bd4')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  # generate R bindings
+  cd "$_pkgname"
+  ./runSwig.sh
+  cd ..
+
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" Rscript --vanilla runTests.R
 }
 
 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-chemminer/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 = "GNU make",
-        print(line)
+    )
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-chemminer/lilac.yaml

@@ -1,10 +1,9 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
+- github: pekkarr
-  email: kuoi@bioarchlinux.org
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-base64enc
-- r-bh
 - r-biocgenerics
 - r-dbi
 - r-digest
@@ -18,8 +17,14 @@ repo_depends:
 - r-rjson
 - r-rsvg
 - r-stringi
+repo_makedepends:
+- r-bh
+- r-rsqlite
+- r-runit
+- r-snow
 update_on:
-- regex: ChemmineR_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: ChemmineR
-  url: https://bioconductor.org/packages/ChemmineR
+  repo: bioc
+  md5: true
 - alias: r

lilac-extensions/lilac_r_utils.py

@@ -8,7 +8,7 @@ def r_update_pkgver_and_pkgrel(newver: str):
     """
     Update _pkgver and pkgrel used in R packages.
 
-    The pkgver variable (without underscore) should be defined as `${_pkgver//[:-]/.}`.
+    The pkgver variable (without underscore) should be defined as `${_pkgver//-/.}`.
     """
     ver_prefix = "_pkgver="
     rel_prefix = "pkgrel="
@@ -285,7 +285,7 @@ def check_optdepends(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
             errors.append(f"Unnecessary optional dependency: {dep}")
 
     for dep in desc.suggests:
-        if (dep not in cfg.default_r_pkgs) and (dep not in pkg.optdepends):
+        if (dep not in cfg.default_r_pkgs) and (dep not in pkg.optdepends) and (dep not in pkg.depends):
             errors.append(f"Missing optional dependency: {dep}")
 
     if len(errors) > 0: