[med-svn] [Git][med-team/sepp][master] Fix build issues

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / sepp


Commits:
17b47f41 by Andreas Tille at 2020-08-14T23:15:31+02:00
Fix build issues

- - - - -


3 changed files:

- + debian/patches/change_java_version_for_ant.patch
- + debian/patches/json_collections.patch
- debian/patches/series


Changes:

=====================================
debian/patches/change_java_version_for_ant.patch
=====================================
@@ -0,0 +1,16 @@
+From: Pierre Gruet <pgtdebian at free.fr>
+Date: Fri, 14 Aug 2020 22:40:28 +0200
+Description: More recent version of Java suppresses some warnings
+Origin: https://lists.debian.org/debian-med/2020/08/msg00104.html
+
+--- a/tools/merge/build.xml
++++ b/tools/merge/build.xml
+@@ -29,7 +29,7 @@
+ 
+   <target name="compile">
+         <mkdir dir="${deploy.home}/classes"/>
+-        <javac srcdir="src" destdir="${deploy.home}/classes" source="1.6" target="1.6" debug="on" >
++        <javac srcdir="src" destdir="${deploy.home}/classes" source="1.8" target="1.8" debug="on" >
+ 	        <classpath refid="classpath"/>
+         </javac>
+   </target>


=====================================
debian/patches/json_collections.patch
=====================================
@@ -0,0 +1,49 @@
+From: Pierre Gruet <pgtdebian at free.fr>
+Date: Fri, 14 Aug 2020 22:40:28 +0200
+Description: Fix build issue
+Origin: https://lists.debian.org/debian-med/2020/08/msg00104.html
+
+--- a/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
++++ b/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
+@@ -312,7 +312,9 @@ public class PPlacerJSONMerger {
+ 						return name1.compareTo(name2);
+ 					}
+ 				});
+-			    sortedPlacements.addAll(resultsPlacements);
++                            for (int i=0 ; i<resultsPlacements.size() ; i++) {
++                              sortedPlacements.add(resultsPlacements.getJSONObject(i));
++                            }
+ 			    resultsPlacements = new JSONArray();
+ 			    resultsPlacements.addAll(sortedPlacements);
+ 			}
+--- a/tools/merge/src/phylolab/taxonamic/JSONMerger.java
++++ b/tools/merge/src/phylolab/taxonamic/JSONMerger.java
+@@ -388,7 +388,9 @@ public class JSONMerger {
+             return (int) o;
+           }
+         });
+-        sortedPlacements.addAll(placements);
++        for (Iterator<JSONArray> it=placements.iterator() ; it.hasNext() ;) {
++          sortedPlacements.add(it.next());
++        }
+         double total = 0;
+         ArrayList < JSONArray > list = new ArrayList < JSONArray > ();
+         for (Iterator < JSONArray > itp = sortedPlacements.iterator(); threshold > total && itp.hasNext();) {          
+@@ -559,7 +561,9 @@ public class JSONMerger {
+           return name1.compareTo(name2);
+         }
+       });
+-      sortedPlacements.addAll(resultsPlacements);
++      for (int i=0 ; i<resultsPlacements.size() ; i++) {
++        sortedPlacements.add(resultsPlacements.getJSONObject(i));
++      }
+       resultsPlacements = new JSONArray();
+       resultsPlacements.addAll(sortedPlacements);
+     }
+@@ -735,4 +739,4 @@ public class JSONMerger {
+       System.exit(1);
+     }
+   }
+-}
+\ No newline at end of file
++}


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
 setup.patch
 use_debian_packaged_guppy_from_pplacer.patch
+change_java_version_for_ant.patch
+json_collections.patch



View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/17b47f41b98f9f0d89d83b4b27adad4e33281651

-- 
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/17b47f41b98f9f0d89d83b4b27adad4e33281651
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