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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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