[med-svn] r15239 - in trunk/packages/logol/trunk/debian: . patches
olivier sallou
osallou-guest at moszumanska.debian.org
Fri Nov 22 10:07:32 UTC 2013
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 <osallou at debian.org> 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 <osallou at debian.org>
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
More information about the debian-med-commit
mailing list