October 2013 - Isis-fish-commits - mailman.cloud.codelutin.com

Jenkins build is unstable: isis-fish #1990
by admin+hudson＠codelutin.com Feb. 14, 2014

Feb. 14, 2014

See <http://ci.nuiton.org/jenkins/job/isis-fish/1990/>

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Jenkins build became unstable: isis-fish » IsisFish #1988
by admin+hudson＠codelutin.com Feb. 14, 2014

Feb. 14, 2014

See <http://ci.nuiton.org/jenkins/job/isis-fish/fr.ifremer$isis-fish/1988/>

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r3825 - in branches/4.0.1: . src/main/assembly src/main/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com Oct. 31, 2013

Oct. 31, 2013

Author: echatellier Date: 2013-10-31 23:54:54 +0100 (Thu, 31 Oct 2013) New Revision: 3825 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3825 Log: Simplify R native library loading (now it's magic) Removed: branches/4.0.1/src/main/assembly/isisfish64.bat branches/4.0.1/src/main/assembly/isisfish64.sh branches/4.0.1/src/main/assembly/x64/ branches/4.0.1/src/main/assembly/x86/ Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/assembly/bin.xml branches/4.0.1/src/main/assembly/isisfish-log4j.properties branches/4.0.1/src/main/assembly/isisfish.bat branches/4.0.1/src/main/assembly/isisfish.sh branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/pom.xml 2013-10-31 22:54:54 UTC (rev 3825) @@ -147,7 +147,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-j2r</artifactId> - <version>1.0.2</version> + <version>1.1-SNAPSHOT</version> <scope>compile</scope> </dependency> Modified: branches/4.0.1/src/main/assembly/bin.xml =================================================================== --- branches/4.0.1/src/main/assembly/bin.xml 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/bin.xml 2013-10-31 22:54:54 UTC (rev 3825) @@ -6,7 +6,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 1999 - 2010 Ifremer, CodeLutin + Copyright (C) 1999 - 2013 Ifremer, CodeLutin, Eric Chatellier %% This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as @@ -31,12 +31,6 @@ <formats> <format>zip</format> </formats> -  <fileSets> <fileSet> @@ -46,12 +40,6 @@ <include>*.jar</include> </includes> </fileSet> -  <fileSet> <includes> <include>README*</include> @@ -66,8 +54,6 @@ <includes> <include>isisfish.sh</include> <include>isisfish.bat</include> - <include>isisfish64.sh</include> - <include>isisfish64.bat</include> </includes> </fileSet> <fileSet> @@ -83,21 +69,5 @@ <file> <source>target/${artifact.artifactId}-${artifact.version}.jar</source> </file> - <file> - <source>src/main/assembly/x86/jri.dll</source> - <outputDirectory>jri</outputDirectory> - </file> - <file> - <source>src/main/assembly/x86/libjri.so</source> - <outputDirectory>jri</outputDirectory> - </file> - <file> - <source>src/main/assembly/x64/jri.dll</source> - <outputDirectory>jri64</outputDirectory> - </file> - <file> - <source>src/main/assembly/x64/libjri.so</source> - <outputDirectory>jri64</outputDirectory> - </file> </files> </assembly> Modified: branches/4.0.1/src/main/assembly/isisfish-log4j.properties =================================================================== --- branches/4.0.1/src/main/assembly/isisfish-log4j.properties 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish-log4j.properties 2013-10-31 22:54:54 UTC (rev 3825) @@ -5,7 +5,7 @@ # $Id$ # $HeadURL$ # %% -# Copyright (C) 2011 - 2012 Ifremer, CodeLutin, Chatellier Eric +# Copyright (C) 2011 - 2013 Ifremer, CodeLutin, Chatellier Eric # %% # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as Modified: branches/4.0.1/src/main/assembly/isisfish.bat =================================================================== --- branches/4.0.1/src/main/assembly/isisfish.bat 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish.bat 2013-10-31 22:54:54 UTC (rev 3825) @@ -5,4 +5,4 @@ rem SET PATH=%PATH%;%R_HOME%\bin\i386 echo [Script] Isis starting... -java -Xmx900M -Djava.library.path=jri -DR.type=jni -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 +java -Xmx900M -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 Modified: branches/4.0.1/src/main/assembly/isisfish.sh =================================================================== --- branches/4.0.1/src/main/assembly/isisfish.sh 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish.sh 2013-10-31 22:54:54 UTC (rev 3825) @@ -1,6 +1,5 @@ #!/bin/bash MEMORY="-Xmx1024M" -JRIARGS="-Djava.library.path=jri -DR.type=jni" -java $MEMORY $JRIARGS -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt +java $MEMORY -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt Deleted: branches/4.0.1/src/main/assembly/isisfish64.bat =================================================================== --- branches/4.0.1/src/main/assembly/isisfish64.bat 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish64.bat 2013-10-31 22:54:54 UTC (rev 3825) @@ -1,8 +0,0 @@ -@echo off - -rem Uncomment following 2 lines to easy configure R for ISIS-Fish -rem SET R_HOME=C:\Program Files\R\R-2.14.1 -rem SET PATH=%PATH%;%R_HOME%\bin\x64 - -echo [Script] Isis starting... -java -Xmx1024M -Djava.library.path=jri64 -DR.type=jni -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 Deleted: branches/4.0.1/src/main/assembly/isisfish64.sh =================================================================== --- branches/4.0.1/src/main/assembly/isisfish64.sh 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish64.sh 2013-10-31 22:54:54 UTC (rev 3825) @@ -1,6 +0,0 @@ -#!/bin/bash - -MEMORY="-Xmx1024M" -JRIARGS="-Djava.library.path=jri64 -DR.type=jni" - -java $MEMORY $JRIARGS -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java 2013-10-31 22:54:54 UTC (rev 3825) @@ -119,16 +119,17 @@ // permet de faire fonctionner la compilation en webstart System.setSecurityManager(null); + // set Rtype in jni mode + System.setProperty("R.type", "jni"); + // i18n is not inited here if (log.isInfoEnabled()) { log.info("Starting Isis-Fish " + IsisConfig.getVersion() + " with args : " + java.util.Arrays.toString(args)); log.info("Date: " + SimpleDateFormat.getInstance().format(new java.util.Date())); log.info("Java version: " + System.getProperty("java.runtime.version") + ", " + System.getProperty("java.vm.name")); - log.info("System arch: " + System.getProperty("os.arch")); - log.info("R_HOME: " + System.getenv("R_HOME") + ", R.type: " + System.getProperty("R.type")); + log.info("Plaform/arch: " + System.getProperty("os.name") + "/" + System.getProperty("os.arch")); + log.info("R_HOME: " + System.getenv("R_HOME")); log.info("PATH: " + System.getenv("PATH")); - log.info("java.library.path: " + System.getProperty("java.library.path")); - } // initialisation de l'application

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r3824 - branches/4.0.1
by echatellier＠users.forge.codelutin.com Oct. 28, 2013

Oct. 28, 2013

Author: echatellier Date: 2013-10-28 18:11:18 +0100 (Mon, 28 Oct 2013) New Revision: 3824 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3824 Log: Use java 7 signature Modified: branches/4.0.1/pom.xml Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-10-28 16:58:02 UTC (rev 3823) +++ branches/4.0.1/pom.xml 2013-10-28 17:11:18 UTC (rev 3824) @@ -472,8 +472,8 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <maven.compiler.source>1.7</maven.compiler.source> <maven.compiler.target>1.7</maven.compiler.target> - <signatureArtifactId>java16</signatureArtifactId> - <signatureVersion>1.1</signatureVersion> + <signatureArtifactId>java17</signatureArtifactId> + <signatureVersion>1.0</signatureVersion>  <jaxxVersion>2.5.28</jaxxVersion>

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r3823 - in branches/4.0.1: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/actions src/main/java/fr/ifremer/isisfish/types/hibernate src/test/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com Oct. 28, 2013

Oct. 28, 2013

Author: echatellier Date: 2013-10-28 17:58:02 +0100 (Mon, 28 Oct 2013) New Revision: 3823 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3823 Log: Update libs Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/pom.xml 2013-10-28 16:58:02 UTC (rev 3823) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>3.4.9</version> + <version>4.1</version> </parent> <groupId>fr.ifremer</groupId> @@ -20,21 +20,21 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>${nuitonUtilsVersion}</version> + <version>2.7.1</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-config</artifactId> - <version>${nuitonUtilsVersion}</version> + <version>3.0-alpha-1</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-validator</artifactId> - <version>${nuitonUtilsVersion}</version> + <version>3.0-alpha-2</version> <scope>compile</scope> </dependency> @@ -90,7 +90,7 @@ <dependency> <groupId>com.fifesoft</groupId> <artifactId>rsyntaxtextarea</artifactId> - <version>2.0.6</version> + <version>2.5.0</version> <scope>runtime</scope> </dependency> @@ -189,7 +189,7 @@ <dependency> <groupId>org.apache.commons</groupId> <artifactId>commons-email</artifactId> - <version>1.3.1</version> + <version>1.3.2</version> </dependency> <dependency> @@ -255,7 +255,7 @@ <dependency> <groupId>com.jcraft</groupId> <artifactId>jsch</artifactId> - <version>0.1.49</version> + <version>0.1.50</version> <scope>compile</scope> </dependency> @@ -288,32 +288,24 @@ <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> - <version>1.3.171</version> + <version>1.3.174</version> <scope>compile</scope> </dependency> -  <dependency> - <groupId>com.h2database</groupId> - <artifactId>h2mig_pagestore_addon</artifactId> - <version>1.3.153</version> - <scope>runtime</scope> - </dependency> - - <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjrt</artifactId> - <version>1.7.2</version> + <version>1.7.3</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.7.2</version> + <version>1.7.3</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjtools</artifactId> - <version>1.7.2</version> + <version>1.7.3</version> </dependency>  @@ -329,7 +321,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.7.8</version> + <version>1.8.0-SNAPSHOT</version> <scope>compile</scope> </dependency>  @@ -337,7 +329,7 @@ <dependency> <groupId>org.freemarker</groupId> <artifactId>freemarker</artifactId> - <version>2.3.19</version> + <version>2.3.20</version> <scope>compile</scope> </dependency> @@ -480,14 +472,15 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <maven.compiler.source>1.7</maven.compiler.source> <maven.compiler.target>1.7</maven.compiler.target> + <signatureArtifactId>java16</signatureArtifactId> + <signatureVersion>1.1</signatureVersion>  - <jaxxVersion>2.5.16</jaxxVersion> - <eugeneVersion>2.6.2</eugeneVersion> - <topiaVersion>2.8-SNAPSHOT</topiaVersion> - <hibernateVersion>4.2.0.Final</hibernateVersion> - <nuitonUtilsVersion>2.6.12</nuitonUtilsVersion> - <nuitonI18nVersion>2.5</nuitonI18nVersion> + <jaxxVersion>2.5.28</jaxxVersion> + <eugeneVersion>2.6.3</eugeneVersion> + <topiaVersion>2.8.1.3</topiaVersion> + <hibernateVersion>4.2.7.Final</hibernateVersion> + <nuitonI18nVersion>2.5.2</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion> <redmine.releaseFiles>target/isis-fish-${project.version}-bin.zip</redmine.releaseFiles> @@ -686,6 +679,10 @@ <id>nuiton.public</id> <url>http://nexus.nuiton.org/nexus/content/groups/public</url> </repository> + <repository> + <id>svnkit.public</id> + <url>http://maven.tmatesoft.com/content/repositories/snapshots</url> + </repository> </repositories> <pluginRepositories> @@ -757,7 +754,7 @@ <artifactId>maven-javadoc-plugin</artifactId> <configuration> <links> - <link>http://download.oracle.com/javase/6/docs/api/</link> + <link>http://docs.oracle.com/javase/7/docs/api/</link> <link>http://maven-site.nuiton.org/nuiton-utils/nuiton-utils/apidocs/</link> <link>http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/</link> <link>http://maven-site.nuiton.org/nuiton-j2r/apidocs/</link> Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -43,8 +43,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.time.DurationFormatUtils; import org.nuiton.math.matrix.DoubleBigVector; -import org.nuiton.util.config.ApplicationConfig; -import org.nuiton.util.config.ConfigOptionDef; +import org.nuiton.config.ApplicationConfig; +import org.nuiton.config.ConfigOptionDef; import org.nuiton.util.StringUtil; import org.nuiton.util.Version; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -36,7 +36,7 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.util.ApplicationConfig.Action.Step; +import org.nuiton.config.ApplicationConfig.Action.Step; import fr.ifremer.isisfish.IsisConfig; import fr.ifremer.isisfish.datastore.SimulationPlanStorage; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -34,7 +34,7 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.util.ApplicationConfig.Action.Step; +import org.nuiton.config.ApplicationConfig.Action.Step; import org.nuiton.util.ZipUtil; import fr.ifremer.isisfish.IsisConfig; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -42,7 +42,7 @@ import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.util.StringUtil; import org.hibernate.HibernateException; -import org.hibernate.engine.SessionImplementor; +import org.hibernate.engine.spi.SessionImplementor; import org.hibernate.engine.jdbc.NonContextualLobCreator; import org.hibernate.type.StandardBasicTypes; import org.hibernate.type.Type; Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -33,7 +33,7 @@ import org.junit.Before; import org.junit.BeforeClass; import org.nuiton.util.FileUtil; -import org.nuiton.util.config.ArgumentsParserException; +import org.nuiton.config.ArgumentsParserException; import fr.ifremer.isisfish.datastore.AutoMigrationIsisH2Config; import fr.ifremer.isisfish.datastore.CodeSourceStorage.Location;

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