Author: osallou-guest Date: 2013-11-22 10:14:27 +0000 (Fri, 22 Nov 2013) New Revision: 15240
Added: trunk/packages/logol/tags/1.6.9-1/ trunk/packages/logol/tags/1.6.9-1/debian/changelog trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath trunk/packages/logol/tags/1.6.9-1/debian/patches/series trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs trunk/packages/logol/tags/1.6.9-1/debian/rules Removed: trunk/packages/logol/tags/1.6.9-1/debian/changelog trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath trunk/packages/logol/tags/1.6.9-1/debian/patches/series trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs trunk/packages/logol/tags/1.6.9-1/debian/rules Log: [svn-buildpackage] Tagging logol 1.6.9-1 Deleted: trunk/packages/logol/tags/1.6.9-1/debian/changelog =================================================================== --- trunk/packages/logol/trunk/debian/changelog 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/changelog 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,93 +0,0 @@ -logol (1.6.5-1) unstable; urgency=low - - * New upstream release (memory footprint optimisation in some cases). - - -- Olivier Sallou <[email protected]> Fri, 25 Oct 2013 13:48:22 +0200 - -logol (1.6.4-1) unstable; urgency=low - - * New upstream release fixing bugs - - -- Olivier Sallou <[email protected]> Tue, 22 Oct 2013 08:35:45 +0200 - -logol (1.6.3-1) unstable; urgency=low - - * New upstream release fixing important bugs on distance search - * Remove patch for doc generation after swi-prolog fix - - -- Olivier Sallou <[email protected]> Mon, 02 Sep 2013 08:54:46 +0200 - -logol (1.6.2-3) unstable; urgency=low - - * Fix swi-prolog compilation (Closes: #719030). - - -- Olivier Sallou <[email protected]> Thu, 08 Aug 2013 10:30:12 +0200 - -logol (1.6.2-2) unstable; urgency=low - - [ Olivier Sallou ] - * Remove deprecated DM-Upload field. - - [ Dmitrijs Ledkovs ] - * Bump standards version to 3.9.4. - * Remove empty postinst script. - * Add dependancy on texlive-latex-extra, needed to fix documentation - FTBFS with new TeX Live. - - -- Dmitrijs Ledkovs <[email protected]> Mon, 03 Jun 2013 23:36:49 +0100 - -logol (1.6.2-1) unstable; urgency=low - - * New upstream release (bug fixes) - - -- Olivier Sallou <[email protected]> Fri, 24 May 2013 14:37:24 +0200 - -logol (1.6.1-1) unstable; urgency=low - - * New upstream release (bug fixes) - - -- Olivier Sallou <[email protected]> Tue, 09 Apr 2013 16:57:33 +0200 - -logol (1.6.0-1) unstable; urgency=low - - * New upstream release with bug fixes - - -- Olivier Sallou <[email protected]> Fri, 15 Feb 2013 10:05:50 +0100 - -logol (1.5.0-6) unstable; urgency=low - - [ Olivier Sallou ] - * debian/control: Fix typo in description (Closes: #685079). - Thanks to Erik Esterer <[email protected]> - - -- Olivier Sallou <[email protected]> Fri, 17 Aug 2012 08:00:58 +0200 - -logol (1.5.0-5) unstable; urgency=low - - [ Olivier Sallou] - * Transition package to use default java implementation: - From [email protected] (Closes: #684158) - - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency - to default-jre | java6-runtime. - - d/rules: Specify source/target = 1.5 to ensure backwards compatible - bytecode is built. - - -- Olivier Sallou <[email protected]> Tue, 07 Aug 2012 15:18:43 +0200 - -logol (1.5.0-4) unstable; urgency=low - - * debian/postinst: remove directory permissions (Closes: #683647). - - -- Olivier Sallou <[email protected]> Thu, 02 Aug 2012 17:09:31 +0200 - -logol (1.5.0-2) unstable; urgency=low - - * Support Arch dependent and arch independent separate builds. - - -- Olivier Sallou <[email protected]> Sun, 01 Jul 2012 23:49:16 +0200 - -logol (1.5.0-1) unstable; urgency=low - - * Initial release (Closes: #678373). - - -- Olivier Sallou <[email protected]> Thu, 21 Jun 2012 12:50:22 +0200 Copied: trunk/packages/logol/tags/1.6.9-1/debian/changelog (from rev 15239, trunk/packages/logol/trunk/debian/changelog) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/changelog (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/changelog 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,106 @@ +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). + + -- Olivier Sallou <[email protected]> Wed, 30 Oct 2013 16:21:09 +0100 + +logol (1.6.5-1) unstable; urgency=low + + * New upstream release (memory footprint optimisation in some cases). + + -- Olivier Sallou <[email protected]> Fri, 25 Oct 2013 13:48:22 +0200 + +logol (1.6.4-1) unstable; urgency=low + + * New upstream release fixing bugs + + -- Olivier Sallou <[email protected]> Tue, 22 Oct 2013 08:35:45 +0200 + +logol (1.6.3-1) unstable; urgency=low + + * New upstream release fixing important bugs on distance search + * Remove patch for doc generation after swi-prolog fix + + -- Olivier Sallou <[email protected]> Mon, 02 Sep 2013 08:54:46 +0200 + +logol (1.6.2-3) unstable; urgency=low + + * Fix swi-prolog compilation (Closes: #719030). + + -- Olivier Sallou <[email protected]> Thu, 08 Aug 2013 10:30:12 +0200 + +logol (1.6.2-2) unstable; urgency=low + + [ Olivier Sallou ] + * Remove deprecated DM-Upload field. + + [ Dmitrijs Ledkovs ] + * Bump standards version to 3.9.4. + * Remove empty postinst script. + * Add dependancy on texlive-latex-extra, needed to fix documentation + FTBFS with new TeX Live. + + -- Dmitrijs Ledkovs <[email protected]> Mon, 03 Jun 2013 23:36:49 +0100 + +logol (1.6.2-1) unstable; urgency=low + + * New upstream release (bug fixes) + + -- Olivier Sallou <[email protected]> Fri, 24 May 2013 14:37:24 +0200 + +logol (1.6.1-1) unstable; urgency=low + + * New upstream release (bug fixes) + + -- Olivier Sallou <[email protected]> Tue, 09 Apr 2013 16:57:33 +0200 + +logol (1.6.0-1) unstable; urgency=low + + * New upstream release with bug fixes + + -- Olivier Sallou <[email protected]> Fri, 15 Feb 2013 10:05:50 +0100 + +logol (1.5.0-6) unstable; urgency=low + + [ Olivier Sallou ] + * debian/control: Fix typo in description (Closes: #685079). + Thanks to Erik Esterer <[email protected]> + + -- Olivier Sallou <[email protected]> Fri, 17 Aug 2012 08:00:58 +0200 + +logol (1.5.0-5) unstable; urgency=low + + [ Olivier Sallou] + * Transition package to use default java implementation: + From [email protected] (Closes: #684158) + - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency + to default-jre | java6-runtime. + - d/rules: Specify source/target = 1.5 to ensure backwards compatible + bytecode is built. + + -- Olivier Sallou <[email protected]> Tue, 07 Aug 2012 15:18:43 +0200 + +logol (1.5.0-4) unstable; urgency=low + + * debian/postinst: remove directory permissions (Closes: #683647). + + -- Olivier Sallou <[email protected]> Thu, 02 Aug 2012 17:09:31 +0200 + +logol (1.5.0-2) unstable; urgency=low + + * Support Arch dependent and arch independent separate builds. + + -- Olivier Sallou <[email protected]> Sun, 01 Jul 2012 23:49:16 +0200 + +logol (1.5.0-1) unstable; urgency=low + + * Initial release (Closes: #678373). + + -- Olivier Sallou <[email protected]> Thu, 21 Jun 2012 12:50:22 +0200 Deleted: trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh =================================================================== --- trunk/packages/logol/trunk/debian/get-orig-source.sh 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,41 +0,0 @@ -#!/bin/bash - -set -e - -PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` -VERSION=`uscan --rename --verbose --force-download | - grep "Newest version on remote site is .* local version is .*" | - head -n 1 | - sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"` - -#VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }'| cut -d"-" -f1` -#svn export svn://scm.gforge.inria.fr/svn/logolexec/trunk/LogolExec ${PKG}-${VERSION}.orig - -mkdir -p ../tarballs -cd ../tarballs - -UTAR="${PKG}_${VERSION}.orig.tar.bz2" -mv ../${UTAR} . -tar xfJ ${UTAR} - -mv ${PKG}-${VERSION} ${PKG}-${VERSION}.orig - -rm -rf ${PKG}-${VERSION}.orig/Doc/uml -rm -f ${PKG}-${VERSION}.orig/Doc/Service* -#mv ${PKG}-${VERSION}.orig/lib/antlrworks-1.4.2.jar . -rm -rf ${PKG}-${VERSION}.orig/lib/* -#mv antlrworks-1.4.2.jar ${PKG}-${VERSION}.orig/lib/ -rm -rf ${PKG}-${VERSION}.orig/Doc/JavaDoc -chmod 755 ${PKG}-${VERSION}.orig/Doc/grammar/*.sh -chmod 755 ${PKG}-${VERSION}.orig/tools/*.sh -rm -f ${PKG}-${VERSION}.orig/Doc/*.mdr* -rm -f ${PKG}-${VERSION}.orig/prolog/*.exe -# Will be regenerated at build time -rm -f ${PKG}-${VERSION}.orig/src/org/irisa/genouest/logol/parser/* -# Will be rewritten from template -rm -f ${PKG}-${VERSION}.orig/tools/suffixSearch.sh - - -BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig - -rm -rf ${PKG}-${VERSION}.orig Copied: trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh (from rev 15239, trunk/packages/logol/trunk/debian/get-orig-source.sh) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/get-orig-source.sh 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,41 @@ +#!/bin/bash + +set -e + +PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +VERSION=`uscan --rename --verbose --force-download | + grep "Newest version on remote site is .* local version is .*" | + head -n 1 | + sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"` + +#VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }'| cut -d"-" -f1` +#svn export svn://scm.gforge.inria.fr/svn/logolexec/trunk/LogolExec ${PKG}-${VERSION}.orig + +mkdir -p ../tarballs +cd ../tarballs + +UTAR="${PKG}_${VERSION}.orig.tar.bz2" +mv ../${UTAR} . +tar xfj ${UTAR} + +mv ${PKG}-${VERSION} ${PKG}-${VERSION}.orig + +rm -rf ${PKG}-${VERSION}.orig/Doc/uml +rm -f ${PKG}-${VERSION}.orig/Doc/Service* +#mv ${PKG}-${VERSION}.orig/lib/antlrworks-1.4.2.jar . +rm -rf ${PKG}-${VERSION}.orig/lib/* +#mv antlrworks-1.4.2.jar ${PKG}-${VERSION}.orig/lib/ +rm -rf ${PKG}-${VERSION}.orig/Doc/JavaDoc +chmod 755 ${PKG}-${VERSION}.orig/Doc/grammar/*.sh +chmod 755 ${PKG}-${VERSION}.orig/tools/*.sh +rm -f ${PKG}-${VERSION}.orig/Doc/*.mdr* +rm -f ${PKG}-${VERSION}.orig/prolog/*.exe +# Will be regenerated at build time +rm -f ${PKG}-${VERSION}.orig/src/org/irisa/genouest/logol/parser/* +# Will be rewritten from template +rm -f ${PKG}-${VERSION}.orig/tools/suffixSearch.sh + + +BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig + +rm -rf ${PKG}-${VERSION}.orig Deleted: trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides =================================================================== --- trunk/packages/logol/trunk/debian/logol.lintian-overrides 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,5 +0,0 @@ -# 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/ Copied: trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides (from rev 15239, trunk/packages/logol/trunk/debian/logol.lintian-overrides) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/logol.lintian-overrides 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,3 @@ +# 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/ Deleted: trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 =================================================================== --- trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,25 +0,0 @@ -Subject: DRMAA API change between 6.1 and 6.2 -Description: Debian DRMAA is v6.2, API need an update -Author: Olivier Sallou <[email protected]> -Last-Updated: 2012-06-18 ---- 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; - - /* - * Manage the submission of jobs on a SGE system using DRMAA Java library. -@@ -76,7 +77,9 @@ - // Redirect DRM streams - 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"); - jobId = session.runJob(jt); - logger.info("Executing job: "+jobId); Copied: trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 (from rev 15239, trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/fixDrmmato6.2 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,34 @@ +Subject: DRMAA API change between 6.1 and 6.2 +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; + + /* + * Manage the submission of jobs on a SGE system using DRMAA Java library. +@@ -80,11 +81,16 @@ + jt.setOutputPath(":" + out+".out"); + 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); Deleted: trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath =================================================================== --- trunk/packages/logol/trunk/debian/patches/fixLibPath 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,57 +0,0 @@ -Subject: Use debian library for generation -Description: Debian libraries should be used -Author: Olivier Sallou <[email protected]> -Last-Updated: 2012-06-18 ---- a/build.xml -+++ b/build.xml -@@ -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"> - - <property environment="env" /> - -@@ -50,6 +50,9 @@ - <fileset dir="${basedir}/lib"> - <patternset refid="java.libs" /> - </fileset> -+ <fileset dir="/usr/share/java" > -+ <patternset refid="java.libs" /> -+ </fileset> - </path> - - -@@ -130,6 +133,25 @@ - <fileset dir="${basedir}/lib"> - <include name="**/*.jar" /> - </fileset> -+ <fileset dir="/usr/share/java" > -+ <include name="biojava.jar"/> -+ <include name="activation.jar"/> -+ <include name="bytecode.jar"/> -+ <include name="drmaa.jar"/> -+ <include name="antlr3-runtime.jar"/> -+ <include name="commons-cli.jar"/> -+ <include name="commons-lang.jar"/> -+ <include name="commons-collections3.jar"/> -+ <include name="commons-configuration.jar"/> -+ <include name="commons-logging.jar"/> -+ <include name="xalan2.jar"/> -+ <include name="xercesImpl.jar"/> -+ <include name="xml-apis.jar"/> -+ <include name="gnumail.jar"/> -+ <include name="log4j-1.2.jar"/> -+ <include name="serializer.jar"/> -+ <include name="junit4.jar"/> -+ </fileset> - </classpath> - <sysproperty key="logol.install" value="${basedir}" /> - <sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" /> -@@ -189,6 +211,7 @@ - <attribute name="Main-Class" value="org.irisa.genouest.logol.Logol" /> - <attribute name="Implementation-Version" value="${version}" /> - <attribute name="Implementation-Build" value="${build.nb}" /> -+ <attribute name="Class-Path" value="/usr/share/java/biojava.jar /usr/share/java/activation.jar /usr/share/java/bytecode.jar /usr/share/java/serializer.jar /usr/share/java/antlr3-runtime.jar /usr/share/java/drmaa.jar /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/xalan2.jar /usr/share/java/xercesImpl.jar /usr/share/java/gnumail.jar /usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" /> - </manifest> - </jar> - </target> Copied: trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath (from rev 15239, trunk/packages/logol/trunk/debian/patches/fixLibPath) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/fixLibPath 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,57 @@ +Subject: Use debian library for generation +Description: Debian libraries should be used +Author: Olivier Sallou <[email protected]> +Last-Updated: 2012-06-18 +--- a/build.xml ++++ b/build.xml +@@ -1,5 +1,5 @@ + <?xml version="1.0" encoding="ISO-8859-1"?> +-<project name="LogolMatch" basedir="." default="create-jar"> ++<project name="LogolMatch" basedir="." default="test_swi"> + + <property environment="env" /> + +@@ -57,6 +57,9 @@ + <fileset dir="${basedir}/lib"> + <patternset refid="java.libs" /> + </fileset> ++ <fileset dir="/usr/share/java" > ++ <patternset refid="java.libs" /> ++ </fileset> + </path> + + +@@ -141,6 +144,25 @@ + <fileset dir="${basedir}/lib"> + <include name="**/*.jar" /> + </fileset> ++ <fileset dir="/usr/share/java" > ++ <include name="biojava.jar"/> ++ <include name="activation.jar"/> ++ <include name="bytecode.jar"/> ++ <include name="drmaa.jar"/> ++ <include name="antlr3-runtime.jar"/> ++ <include name="commons-cli.jar"/> ++ <include name="commons-lang.jar"/> ++ <include name="commons-collections3.jar"/> ++ <include name="commons-configuration.jar"/> ++ <include name="commons-logging.jar"/> ++ <include name="xalan2.jar"/> ++ <include name="xercesImpl.jar"/> ++ <include name="xml-apis.jar"/> ++ <include name="gnumail.jar"/> ++ <include name="log4j-1.2.jar"/> ++ <include name="serializer.jar"/> ++ <include name="junit4.jar"/> ++ </fileset> + </classpath> + <sysproperty key="logol.install" value="${basedir}" /> + <sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" /> +@@ -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}" /> ++ <attribute name="Class-Path" value="/usr/share/java/biojava.jar /usr/share/java/activation.jar /usr/share/java/bytecode.jar /usr/share/java/serializer.jar /usr/share/java/antlr3-runtime.jar /usr/share/java/drmaa.jar /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/xalan2.jar /usr/share/java/xercesImpl.jar /usr/share/java/gnumail.jar /usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" /> + </manifest> + </jar> + </target> Deleted: trunk/packages/logol/tags/1.6.9-1/debian/patches/series =================================================================== --- trunk/packages/logol/trunk/debian/patches/series 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/series 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,5 +0,0 @@ -fixLibPath -fixDrmmato6.2 -setDebianDirs -fix_doc_generation -fix_swipl_module_declaration Copied: trunk/packages/logol/tags/1.6.9-1/debian/patches/series (from rev 15239, trunk/packages/logol/trunk/debian/patches/series) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/patches/series (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/series 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,4 @@ +fixLibPath +fixDrmmato6.2 +setDebianDirs +fix_doc_generation Deleted: trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs =================================================================== --- trunk/packages/logol/trunk/debian/patches/setDebianDirs 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,55 +0,0 @@ -Subject: Use debian dirs for logs -Description: Debian policy hierarchy use -Author: Olivier Sallou <[email protected]> -Last-Updated: 2012-06-18 ---- a/log4j.properties -+++ b/log4j.properties -@@ -13,6 +13,6 @@ - - - log4j.appender.A2=org.apache.log4j.FileAppender --log4j.appender.A2.File=/home/osallou/CODE/TEST/logol.log -+log4j.appender.A2.File=/var/log/logol/logol.log - log4j.appender.A2.layout=org.apache.log4j.PatternLayout --log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n -\ No newline at end of file -+log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n ---- a/prolog/logol.properties -+++ b/prolog/logol.properties -@@ -11,9 +11,9 @@ - #maxMatchSize=30000 - maxMatchSize=0 - # Temporary directory used for the analysis. Should be local to the node --workingDir=/tmp/Logol -+workingDir=/tmp/ - # Directory where to place the results. In case of cluster usage, result must be a shared directory between nodes --dir.result=/tmp/Logol -+dir.result=/var/lib/logol/results/ - # Maximum length of a spacer when looking forward for a match - #maxSpacerLength=10000 - maxSpacerLength=0 -@@ -42,4 +42,4 @@ - # Use Vmatch [1] or internal tool [0] (default) - suffix.tool = 0 - # Vmatch path, if used nad not in path --suffix.path= -\ No newline at end of file -+suffix.path= ---- a/LogolExec.sh -+++ b/LogolExec.sh -@@ -17,5 +17,5 @@ - - 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 $LOGOL_HOME/lib/biojava.jar:$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 $* - ---- a/LogolMultiExec.sh -+++ b/LogolMultiExec.sh -@@ -20,5 +20,5 @@ - - echo "calling logol with parameters "$* - --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 $* - Copied: trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs (from rev 15239, trunk/packages/logol/trunk/debian/patches/setDebianDirs) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/patches/setDebianDirs 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,55 @@ +Subject: Use debian dirs for logs +Description: Debian policy hierarchy use +Author: Olivier Sallou <[email protected]> +Last-Updated: 2012-06-18 +--- a/log4j.properties ++++ b/log4j.properties +@@ -13,6 +13,6 @@ + + + log4j.appender.A2=org.apache.log4j.FileAppender +-log4j.appender.A2.File=/home/osallou/CODE/TEST/logol.log ++log4j.appender.A2.File=/var/log/logol/logol.log + log4j.appender.A2.layout=org.apache.log4j.PatternLayout +-log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n +\ No newline at end of file ++log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n +--- a/prolog/logol.properties ++++ b/prolog/logol.properties +@@ -11,9 +11,9 @@ + #maxMatchSize=30000 + maxMatchSize=0 + # Temporary directory used for the analysis. Should be local to the node +-workingDir=/tmp/Logol ++workingDir=/tmp/ + # Directory where to place the results. In case of cluster usage, result must be a shared directory between nodes +-dir.result=/tmp/Logol ++dir.result=/var/lib/logol/results/ + # Maximum length of a spacer when looking forward for a match + #maxSpacerLength=10000 + maxSpacerLength=0 +@@ -42,4 +42,4 @@ + # Use Vmatch [1] or internal tool [0] (default) + suffix.tool = 0 + # Vmatch path, if used nad not in path +-suffix.path= +\ No newline at end of file ++suffix.path= +--- a/LogolExec.sh ++++ b/LogolExec.sh +@@ -21,5 +21,5 @@ + LOGOL_LOG4J=$LOGOL_HOME/log4j.properties + fi + +-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 $* + +--- a/LogolMultiExec.sh ++++ b/LogolMultiExec.sh +@@ -25,5 +25,5 @@ + + echo "calling logol with parameters "$* + +-java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_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 $* + Deleted: trunk/packages/logol/tags/1.6.9-1/debian/rules =================================================================== --- trunk/packages/logol/trunk/debian/rules 2013-10-30 14:35:55 UTC (rev 15070) +++ trunk/packages/logol/tags/1.6.9-1/debian/rules 2013-11-22 10:14:27 UTC (rev 15240) @@ -1,47 +0,0 @@ -#!/usr/bin/make -f -# -*- makefile -*- - -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -DEB_ANT_BUILD_TARGET=create-jar,test_swi -DEB_ANT_ARGS=-Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 - -%: - dh $@ - -override_dh_auto_build: - mv tools/pldoc.sty tools/pldoc.sty.upstream - dh_auto_build -- $(DEB_ANT_ARGS) - ant -f build.xml doc - -override_dh_install: - dh_install - 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 - 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 - if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/mycostfunction; fi - -override_dh_clean: - if [ -e tools/pldoc.sty.upstream ]; then mv tools/pldoc.sty.upstream tools/pldoc.sty; fi - dh_clean - rm -f Swi*.xml - rm -f prolog/*.exe - rm -f lib/*.jar - rm -f *.log - rm -f src/org/irisa/genouest/logol/parser/* - rm -f tools/suffixSearch.sh - -override_dh_installexamples: - rm -f test/tmp/* - rm -f test/results/* - dh_installexamples - -override_dh_strip: - dh_strip -Xlogol.exe -Xpreanalyse.exe - -get-orig-source: - debian/get-orig-source.sh Copied: trunk/packages/logol/tags/1.6.9-1/debian/rules (from rev 15239, trunk/packages/logol/trunk/debian/rules) =================================================================== --- trunk/packages/logol/tags/1.6.9-1/debian/rules (rev 0) +++ trunk/packages/logol/tags/1.6.9-1/debian/rules 2013-11-22 10:14:27 UTC (rev 15240) @@ -0,0 +1,48 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +DEB_ANT_BUILD_TARGET=create-jar,test_swi +DEB_ANT_ARGS=-Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 + +%: + dh $@ + +override_dh_auto_build: + mv tools/pldoc.sty tools/pldoc.sty.upstream + dh_auto_build -- $(DEB_ANT_ARGS) + ant -f build.xml doc + +override_dh_install: + dh_install + 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 + if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/mycostfunction; fi + +override_dh_clean: + if [ -e tools/pldoc.sty.upstream ]; then mv tools/pldoc.sty.upstream tools/pldoc.sty; fi + dh_clean + rm -f Swi*.xml + rm -f prolog/*.exe + rm -f lib/*.jar + rm -f *.log + rm -f src/org/irisa/genouest/logol/parser/* + rm -f tools/suffixSearch.sh + +override_dh_installexamples: + rm -f test/tmp/* + rm -f test/results/* + dh_installexamples + +override_dh_strip: + dh_strip -Xlogol.exe -Xpreanalyse.exe + +get-orig-source: + debian/get-orig-source.sh _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
