Author: osallou Date: 2017-09-15 15:28:08 +0000 (Fri, 15 Sep 2017) New Revision: 24047
Added: trunk/packages/rdp-classifier/trunk/debian/patches/ trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch trunk/packages/rdp-classifier/trunk/debian/patches/series Modified: trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier trunk/packages/rdp-classifier/trunk/debian/changelog trunk/packages/rdp-classifier/trunk/debian/control trunk/packages/rdp-classifier/trunk/debian/junit.xml trunk/packages/rdp-classifier/trunk/debian/rules Log: fix java 9 compilation Modified: trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier 2017-09-15 10:01:30 UTC (rev 24046) +++ trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier 2017-09-15 15:28:08 UTC (rev 24047) @@ -14,4 +14,4 @@ JAR=/usr/share/rdp-classifier/rdp_classifier.jar -exec java -Xms512M -Xmx512M -jar "$JAR" "$@" +exec java $JAVA_OPTS -Xms512M -Xmx512M -jar "$JAR" "$@" Modified: trunk/packages/rdp-classifier/trunk/debian/changelog =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/changelog 2017-09-15 10:01:30 UTC (rev 24046) +++ trunk/packages/rdp-classifier/trunk/debian/changelog 2017-09-15 15:28:08 UTC (rev 24047) @@ -1,3 +1,11 @@ +rdp-classifier (2.10.2-2) UNRELEASED; urgency=medium + + * d/control,d/junit.xml: fixes for Java 9 compilation (Closes #875789). + * debian/bin/rdp_classifier: add optional env variable JAVA_OPTS + to java command line + + -- Olivier Sallou <osal...@debian.org> Fri, 15 Sep 2017 13:25:30 +0000 + rdp-classifier (2.10.2-1) unstable; urgency=medium * Initial upload to Debian (Closes: #790926) Modified: trunk/packages/rdp-classifier/trunk/debian/control =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/control 2017-09-15 10:01:30 UTC (rev 24046) +++ trunk/packages/rdp-classifier/trunk/debian/control 2017-09-15 15:28:08 UTC (rev 24047) @@ -15,7 +15,8 @@ librdp-taxonomy-tree-java (>= 1.2.0), libjfreechart-java, ant, - ant-optional + ant-optional, + ant-contrib Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rdp-classifier/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rdp-classifier/trunk/ Modified: trunk/packages/rdp-classifier/trunk/debian/junit.xml =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/junit.xml 2017-09-15 10:01:30 UTC (rev 24046) +++ trunk/packages/rdp-classifier/trunk/debian/junit.xml 2017-09-15 15:28:08 UTC (rev 24047) @@ -1,21 +1,44 @@ <!-- Snippet to drive junit tests in deb build. Build rdp-readseq.jar first. --> <project> <target name="junit"> + <taskdef resource="net/sf/antcontrib/antlib.xml"> + <classpath> + <pathelement location="/usr/share/java/ant-contrib.jar" /> + </classpath> + </taskdef> + <property name="cp" value="rdp_classifier.jar:/usr/share/java/junit4.jar:test"/> - <javac srcdir="test"> + <javac srcdir="test" source="1.8" target="1.8"> <classpath path="${cp}"/> </javac> - <junit printsummary="yes" haltonfailure="yes" showoutput="yes"> - <classpath path="${cp}"/> + <echo>Using java version ${java.version}</echo> + <if><equals arg1="${ant.java.version}" arg2="1.8" /> + <then> + <junit haltonfailure="yes" printsummary="yes" showoutput="true"> + <classpath path="${cp}"/> <formatter type="xml"/> <batchtest fork="yes"> <fileset dir="test" includes="**/rrnaclassifier/**/*Test.java"/> + </batchtest> + </junit> + </then> + <else> + <junit haltonfailure="yes" printsummary="yes" showoutput="true"> + <jvmarg line="--add-modules java.se.ee"/> + <classpath path="${cp}"/> + + <formatter type="xml"/> + + <batchtest fork="yes"> + <fileset dir="test" includes="**/rrnaclassifier/**/*Test.java"/> </batchtest> </junit> + </else> + </if> </target> </project> Added: trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch (rev 0) +++ trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch 2017-09-15 15:28:08 UTC (rev 24047) @@ -0,0 +1,78 @@ +Subject: fix resource loading for Java 9 +Description: resource loading modification for Java 9 +Author: Olivier Sallou +Forwarded: no +Last-Updated: 2017-09-15 +--- a/test/edu/msu/cme/rdp/classifier/rrnaclassifier/TrainingInfoTest.java ++++ b/test/edu/msu/cme/rdp/classifier/rrnaclassifier/TrainingInfoTest.java +@@ -55,7 +55,7 @@ + /** Test of createLogWordPriorArr method, of class classification.TrainingInfo. */ + public void testCreateLogWordPriorArr() throws Exception{ + System.out.println("testCreateLogWordPriorArr"); +- InputStream dstream = System.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt"); ++ InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt"); + Reader in = new InputStreamReader( dstream ); + + TrainingInfo train = new TrainingInfo(); +@@ -82,7 +82,7 @@ + /** Test of createGenusWordProbLis method, of class classification.TrainingInfo. */ + public void testCreateGenusWordProbList() throws Exception{ + System.out.println("testCreateGenusWordConditionalProbList"); +- InputStream dstream = System.class.getResourceAsStream("/test/classifier/testGenus_probList.txt"); ++ InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testGenus_probList.txt"); + Reader in = new InputStreamReader( dstream ); + TrainingInfo train = new TrainingInfo(); + train.createGenusWordProbList(in); +@@ -104,7 +104,7 @@ + /** Test of makeProbIndexArr method, of class classification.TrainingInfo. */ + public void testCreateProbIndexArr() throws Exception { + System.out.println("testCreateProbIndexArr"); +- InputStream dstream = System.class.getResourceAsStream("/test/classifier/testProbIndex.txt"); ++ InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testProbIndex.txt"); + Reader in = new InputStreamReader( dstream ); + TrainingInfo train = new TrainingInfo(); + train.createProbIndexArr(in); +@@ -120,19 +120,19 @@ + System.out.println("testCreateClassifier"); + TrainingInfo train = new TrainingInfo(); + +- InputStream dstream = System.class.getResourceAsStream("/test/classifier/testGenus_probList.txt"); ++ InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testGenus_probList.txt"); + Reader in = new InputStreamReader( dstream ); + train.createGenusWordProbList(in); + +- dstream = System.class.getResourceAsStream("/test/classifier/test_bergeyTrainingTree.xml"); ++ dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/test_bergeyTrainingTree.xml"); + in = new InputStreamReader( dstream ); + train.createTree(in); + +- dstream = System.class.getResourceAsStream("/test/classifier/testProbIndex.txt"); ++ dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testProbIndex.txt"); + in = new InputStreamReader( dstream ); + train.createProbIndexArr(in); + +- dstream = System.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt"); ++ dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt"); + in = new InputStreamReader( dstream ); + train.createLogWordPriorArr(in); + +@@ -187,7 +187,7 @@ + + + // end of +- dstream = System.class.getResourceAsStream("/test/classifier/testQuerySeq.fasta"); ++ dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testQuerySeq.fasta"); + in = new InputStreamReader( dstream ); + BufferedReader infile = new BufferedReader(in); + // test the first sequence +--- a/test/edu/msu/cme/rdp/classifier/rrnaclassifier/TreeFileParserTest.java ++++ b/test/edu/msu/cme/rdp/classifier/rrnaclassifier/TreeFileParserTest.java +@@ -39,7 +39,7 @@ + public void testParseTreeFile() throws Exception{ + System.out.println("testParseTreeFile"); + TreeFileParser parser = new TreeFileParser(); +- InputStream dstream = System.class.getResourceAsStream("/test/classifier/testTreeFile.xml"); ++ InputStream dstream = TreeFileParserTest.class.getResourceAsStream("/test/classifier/testTreeFile.xml"); + HierarchyVersion hVersion = null; + + Reader in = new InputStreamReader( dstream ); Added: trunk/packages/rdp-classifier/trunk/debian/patches/series =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/patches/series (rev 0) +++ trunk/packages/rdp-classifier/trunk/debian/patches/series 2017-09-15 15:28:08 UTC (rev 24047) @@ -0,0 +1 @@ +fix_java9_compilation.patch Modified: trunk/packages/rdp-classifier/trunk/debian/rules =================================================================== --- trunk/packages/rdp-classifier/trunk/debian/rules 2017-09-15 10:01:30 UTC (rev 24046) +++ trunk/packages/rdp-classifier/trunk/debian/rules 2017-09-15 15:28:08 UTC (rev 24047) @@ -12,6 +12,7 @@ override_dh_auto_build: jh_build -J rdp_classifier.jar src #jar uf rdp_classifier.jar data + #jar uf rdp_classifier.jar -C test test override_dh_auto_clean: rm -f *.jar lib/*.jar TEST-* _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit