Author: osallou-guest Date: 2013-11-22 10:07:32 +0000 (Fri, 22 Nov 2013) New Revision: 15239
Modified: trunk/packages/logol/trunk/debian/changelog trunk/packages/logol/trunk/debian/get-orig-source.sh trunk/packages/logol/trunk/debian/logol.lintian-overrides trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 trunk/packages/logol/trunk/debian/patches/fixLibPath trunk/packages/logol/trunk/debian/patches/series trunk/packages/logol/trunk/debian/patches/setDebianDirs trunk/packages/logol/trunk/debian/rules Log: new upstream release 1.6.9 Modified: trunk/packages/logol/trunk/debian/changelog =================================================================== --- trunk/packages/logol/trunk/debian/changelog 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/changelog 2013-11-22 10:07:32 UTC (rev 15239) @@ -1,3 +1,10 @@ +logol (1.6.9-1) unstable; urgency=low + + * New upstream release (bug fixes, add Windows support + for Sicstus 4.2.x and Swi-prolog). + + -- Olivier Sallou <[email protected]> Mon, 11 Nov 2013 10:11:17 +0100 + logol (1.6.6-1) unstable; urgency=low * New upstream releas (bug fixes on morphisms and doc). Modified: trunk/packages/logol/trunk/debian/get-orig-source.sh =================================================================== --- trunk/packages/logol/trunk/debian/get-orig-source.sh 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/get-orig-source.sh 2013-11-22 10:07:32 UTC (rev 15239) @@ -16,7 +16,7 @@ UTAR="${PKG}_${VERSION}.orig.tar.bz2" mv ../${UTAR} . -tar xfJ ${UTAR} +tar xfj ${UTAR} mv ${PKG}-${VERSION} ${PKG}-${VERSION}.orig Modified: trunk/packages/logol/trunk/debian/logol.lintian-overrides =================================================================== --- trunk/packages/logol/trunk/debian/logol.lintian-overrides 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/logol.lintian-overrides 2013-11-22 10:07:32 UTC (rev 15239) @@ -1,5 +1,3 @@ -# This is a template, not used by upstream program -logol: executable-not-elf-or-script usr/share/logol/tools/suffixSearchTpl.sh # Work directories required for examples to run logol: package-contains-empty-directory usr/share/doc/logol/examples/results/ logol: package-contains-empty-directory usr/share/doc/logol/examples/tmp/ Modified: trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 =================================================================== --- trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 2013-11-22 10:07:32 UTC (rev 15239) @@ -2,24 +2,33 @@ Description: Debian DRMAA is v6.2, API need an update Author: Olivier Sallou <[email protected]> Last-Updated: 2012-06-18 +Forwarded: no --- a/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java +++ b/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java @@ -10,6 +10,7 @@ import org.ggf.drmaa.Session; import org.ggf.drmaa.SessionFactory; import org.irisa.genouest.logol.Constants; -+import java.util.Arrays; ++import java.util.Arrays; /* * Manage the submission of jobs on a SGE system using DRMAA Java library. -@@ -76,7 +77,9 @@ - // Redirect DRM streams +@@ -80,11 +81,16 @@ jt.setOutputPath(":" + out+".out"); - jt.setErrorPath(":" + out + ".err"); -- jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); -+ String[] tmpargs = new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}; -+ jt.setArgs(Arrays.asList(tmpargs)); -+ // DRMAA 6.1 jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); - jt.setRemoteCommand(installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.sh"); + jt.setErrorPath(":" + out + ".err"); + if(OS.startsWith("win")) { +- jt.setArgs(new String[] {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); ++ //jt.setArgs(new String[] {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); ++ String[] tmpargs = new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}; ++ jt.setArgs(Arrays.asList(tmpargs)); + jt.setRemoteCommand("ruby"); + } + else { +- jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); ++ //jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); ++ String[] tmpargs = new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}; ++ jt.setArgs(Arrays.asList(tmpargs)); ++ + jt.setRemoteCommand(installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.sh"); + } jobId = session.runJob(jt); - logger.info("Executing job: "+jobId); Modified: trunk/packages/logol/trunk/debian/patches/fixLibPath =================================================================== --- trunk/packages/logol/trunk/debian/patches/fixLibPath 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/patches/fixLibPath 2013-11-22 10:07:32 UTC (rev 15239) @@ -7,11 +7,11 @@ @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="ISO-8859-1"?> -<project name="LogolMatch" basedir="." default="create-jar"> -+<project name="LogolMatch" basedir="." default="dist"> ++<project name="LogolMatch" basedir="." default="test_swi"> <property environment="env" /> - -@@ -50,6 +50,9 @@ + +@@ -57,6 +57,9 @@ <fileset dir="${basedir}/lib"> <patternset refid="java.libs" /> </fileset> @@ -21,7 +21,7 @@ </path> -@@ -130,6 +133,25 @@ +@@ -141,6 +144,25 @@ <fileset dir="${basedir}/lib"> <include name="**/*.jar" /> </fileset> @@ -47,7 +47,7 @@ </classpath> <sysproperty key="logol.install" value="${basedir}" /> <sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" /> -@@ -189,6 +211,7 @@ +@@ -200,6 +222,7 @@ <attribute name="Main-Class" value="org.irisa.genouest.logol.Logol" /> <attribute name="Implementation-Version" value="${version}" /> <attribute name="Implementation-Build" value="${build.nb}" /> Modified: trunk/packages/logol/trunk/debian/patches/series =================================================================== --- trunk/packages/logol/trunk/debian/patches/series 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/patches/series 2013-11-22 10:07:32 UTC (rev 15239) @@ -2,4 +2,3 @@ fixDrmmato6.2 setDebianDirs fix_doc_generation -fix_swipl_module_declaration Modified: trunk/packages/logol/trunk/debian/patches/setDebianDirs =================================================================== --- trunk/packages/logol/trunk/debian/patches/setDebianDirs 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/patches/setDebianDirs 2013-11-22 10:07:32 UTC (rev 15239) @@ -37,19 +37,19 @@ +suffix.path= --- a/LogolExec.sh +++ b/LogolExec.sh -@@ -17,5 +17,5 @@ +@@ -21,5 +21,5 @@ + LOGOL_LOG4J=$LOGOL_HOME/log4j.properties + fi - echo "calling logol with parameters "$* +-java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.Logol $* ++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar org.irisa.genouest.logol.Logol $* --java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.Logol $* -+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar org.irisa.genouest.logol.Logol $* - --- a/LogolMultiExec.sh +++ b/LogolMultiExec.sh -@@ -20,5 +20,5 @@ +@@ -25,5 +25,5 @@ echo "calling logol with parameters "$* --java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.dispatcher.Dispatch $* -+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar org.irisa.genouest.logol.dispatcher.Dispatch $* +-java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.dispatcher.Dispatch $* ++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar org.irisa.genouest.logol.dispatcher.Dispatch $* Modified: trunk/packages/logol/trunk/debian/rules =================================================================== --- trunk/packages/logol/trunk/debian/rules 2013-11-22 08:23:49 UTC (rev 15238) +++ trunk/packages/logol/trunk/debian/rules 2013-11-22 10:07:32 UTC (rev 15239) @@ -20,6 +20,7 @@ rm -f debian/logol/usr/share/logol/prolog/*.c rm -f debian/logol/usr/share/logol/prolog/*.exe rm -f debian/logol/usr/share/logol/prolog/logol.properties + rm -f debian/logol/usr/share/logol/tools/*.keep_old_script if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/*.sh; fi if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/*.sh; fi if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/*.rb; fi _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
