From 137c1ffe5ddf478fe4512100f30c8d0d638ba0da Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Thu, 13 Jul 2023 20:50:01 +0300
Subject: [PATCH] r-annotate: use metadata checks

---
 BioArchLinux/r-annotate/PKGBUILD   | 31 ++++++++++++++++++++----------
 BioArchLinux/r-annotate/lilac.py   | 11 ++++++-----
 BioArchLinux/r-annotate/lilac.yaml | 14 +++++++++-----
 lilac-extensions/lilac_r_utils.py  |  2 +-
 4 files changed, 37 insertions(+), 21 deletions(-)

diff --git a/BioArchLinux/r-annotate/PKGBUILD b/BioArchLinux/r-annotate/PKGBUILD
index 6b49df2818..e28afc45bd 100644
--- a/BioArchLinux/r-annotate/PKGBUILD
+++ b/BioArchLinux/r-annotate/PKGBUILD
@@ -1,16 +1,17 @@
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Nick B <Shirakawasuna at gmail _dot_com>
 
 _pkgname=annotate
 _pkgver=1.78.0
 pkgname=r-${_pkgname,,}
-pkgver=1.78.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Annotation for microarrays'
-arch=('any')
+pkgdesc="Annotation for microarrays"
+arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  r
   r-annotationdbi
   r-biobase
   r-biocgenerics
@@ -19,6 +20,10 @@ depends=(
   r-xml
   r-xtable
 )
+checkdepends=(
+  r-org.hs.eg.db
+  r-runit
+)
 optdepends=(
   r-biostrings
   r-genefilter
@@ -35,14 +40,20 @@ optdepends=(
   r-tkwidgets
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('fb5187ca7fdd4e1be47a470d528397df')
 sha256sums=('7e27007dc61ebc140ad722b5c9bb886e39499120b8f6240652df0edfa4c90484')
 
 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 annotate_unit_tests.R
 }
 
 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:
diff --git a/BioArchLinux/r-annotate/lilac.py b/BioArchLinux/r-annotate/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-annotate/lilac.py
+++ b/BioArchLinux/r-annotate/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()
diff --git a/BioArchLinux/r-annotate/lilac.yaml b/BioArchLinux/r-annotate/lilac.yaml
index 7baf701c68..7ee9a6f60a 100644
--- a/BioArchLinux/r-annotate/lilac.yaml
+++ b/BioArchLinux/r-annotate/lilac.yaml
@@ -1,7 +1,7 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-annotationdbi
 - r-biobase
@@ -10,8 +10,12 @@ repo_depends:
 - r-httr
 - r-xml
 - r-xtable
+repo_makedepends:
+- r-org.hs.eg.db
+- r-runit
 update_on:
-- regex: annotate_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/annotate
+- source: rpkgs
+  pkgname: annotate
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py
index 55e4625b5f..8251542cd1 100644
--- a/lilac-extensions/lilac_r_utils.py
+++ b/lilac-extensions/lilac_r_utils.py
@@ -101,7 +101,7 @@ class Description:
             if i != -1:
                 dep = dep[:i]
             dep = dep.strip()
-            if dep != "R":
+            if dep != "R" and len(dep) > 0:
                 ret.append(self._r_name_to_arch(dep))
         return ret