From 6df3d43893bc0165256326299f0a3f87448602fc Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sat, 22 Jul 2023 13:01:34 +0300
Subject: [PATCH] r-chemmineob: use metadata checks

---
 BioArchLinux/r-chemmineob/PKGBUILD   | 42 ++++++++++++++++++----------
 BioArchLinux/r-chemmineob/lilac.py   | 15 ++++++----
 BioArchLinux/r-chemmineob/lilac.yaml | 20 +++++++++----
 3 files changed, 51 insertions(+), 26 deletions(-)

diff --git a/BioArchLinux/r-chemmineob/PKGBUILD b/BioArchLinux/r-chemmineob/PKGBUILD
index eb9966d813..3e8291051a 100644
--- a/BioArchLinux/r-chemmineob/PKGBUILD
+++ b/BioArchLinux/r-chemmineob/PKGBUILD
@@ -1,44 +1,56 @@
-# system requirements: OpenBabel (>= 3.0.0) with headers(http://openbabel.org). Eigen3 with headers.
-# 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=ChemmineOB
 _pkgver=1.38.0
 pkgname=r-${_pkgname,,}
-pkgver=1.38.0
+pkgver=${_pkgver//-/.}
 pkgrel=3
-pkgdesc='R interface to a subset of OpenBabel functionalities'
-arch=('x86_64')
+pkgdesc="R interface to a subset of OpenBabel functionalities"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('custom')
+license=(Artistic2.0 GPL3)
 depends=(
-  r
-  r-bh
+  openbabel
   r-biocgenerics
   r-rcpp
   r-zlibbioc
-  openbabel
+)
+makedepends=(
   eigen
+  r-bh
+)
+checkdepends=(
+  r-chemminer
+  r-runit
 )
 optdepends=(
   r-biocmanager
   r-biocstyle
   r-chemminer
-  r-chemminer
   r-knitr
   r-knitrbootstrap
   r-rmarkdown
   r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5d721ca0fa36f8b42fecca0ab4f98910')
 sha256sums=('9115e25d3be94148fcc549b22af107c3fe0055569ac4e36ce161a203a8698450')
 
 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" Rscript --vanilla runTests.R
 }
 
 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:
diff --git a/BioArchLinux/r-chemmineob/lilac.py b/BioArchLinux/r-chemmineob/lilac.py
index bd219c037c..b28e33abea 100644
--- a/BioArchLinux/r-chemmineob/lilac.py
+++ b/BioArchLinux/r-chemmineob/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 = "file LICENSE",
+        expect_systemrequirements = "OpenBabel (>= 3.0.0) with headers (http://openbabel.org). Eigen3 with headers.",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-chemmineob/lilac.yaml b/BioArchLinux/r-chemmineob/lilac.yaml
index 9291113ca6..902c93f742 100644
--- a/BioArchLinux/r-chemmineob/lilac.yaml
+++ b/BioArchLinux/r-chemmineob/lilac.yaml
@@ -1,14 +1,22 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
-- r-bh
 - r-biocgenerics
 - r-rcpp
 - r-zlibbioc
+repo_makedepends:
+- r-bh
+- r-chemminer
+- r-runit
 update_on:
-- regex: ChemmineOB_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ChemmineOB
+- source: rpkgs
+  pkgname: ChemmineOB
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpmfiles
+  pkgname: openbabel
+  filename: usr/lib/libopenbabel\.so\.([^.]+)
+  repo: extra