Initial Messages

[INFO] Scanning for projects... [INFO] Reactor build order: [INFO] biojava [INFO] bytecode [INFO] core [INFO] alignment [INFO] blast [INFO] biojava structure [INFO] das [INFO] sequence [INFO] sequence-core [INFO] sequence-dna [INFO] sequence-rna [INFO] sequence-biosql [INFO] sequence-fasta [INFO] sequence-blastxml [INFO] sequencing [INFO] phylo [INFO] biosql [INFO] gui [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] task-segment: [site] [INFO] ------------------------------------------------------------------------ [INFO] Setting property: classpath.resource.loader.class => 'org.codehaus.plexus.velocity.ContextClassLoaderResourceLoader'. [INFO] Setting property: velocimacro.messages.on => 'false'. [INFO] Setting property: resource.loader => 'classpath'. [INFO] Setting property: resource.manager.logwhenfound => 'false'. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [INFO] Preparing javadoc:test-javadoc [INFO] No goals needed for project - skipping [INFO] Preparing javadoc:aggregate [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building bytecode [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building core [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building alignment [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building blast [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava structure [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building das [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-core [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-dna [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-rna [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-biosql [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-fasta [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-blastxml [INFO] ------------------------------------------------------------------------

jaxb2:generate {execution: default}

Cannot find CatalogManager.properties [INFO] Skipped XJC execution. Generated sources were up-to-date. [INFO] ------------------------------------------------------------------------ [INFO] Building sequencing [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building phylo [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biosql [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building gui [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] Preparing javadoc:javadoc [INFO] No goals needed for project - skipping [INFO] Preparing javadoc:test-aggregate [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building bytecode [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/bytecode/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building core [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 29 resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building alignment [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/alignment/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building blast [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 3 resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building biojava structure [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 1 resource

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building das [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/das/src/main/resources [WARNING] While downloading xerces:xerces:2.4.0 This artifact has been relocated to xerces:xercesImpl:2.4.0.

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-core [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-dna [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-dna/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-rna [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-rna/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-biosql [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-biosql/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Compiling 1 source file to /home/andreas/src/biojava-svn/sequence/sequence-biosql/target/classes [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-fasta [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-fasta/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-blastxml [INFO] ------------------------------------------------------------------------

jaxb2:generate {execution: default}

[INFO] Skipped XJC execution. Generated sources were up-to-date.

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 3 resources [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] Copying 0 resource [INFO] Copying 1 resource

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequencing [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequencing/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building phylo [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/phylo/src/main/resources [WARNING] While downloading jgrapht:jgrapht:0.7.3 This artifact has been relocated to org.jgrapht:jgrapht-jdk1.5:0.7.3.

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building biosql [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/biosql/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building gui [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/gui/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date

site:site {execution: default-site}

[INFO] Skipped "JavaDocs" report, file "apidocs/index.html" already exists for the English version. [INFO] Skipped "Test JavaDocs" report, file "testapidocs/index.html" already exists for the English version. [INFO] Generating "Issue Tracking" report. [INFO] Generating "Project Summary" report. [INFO] Generating "Mailing Lists" report. [INFO] Generating "Source Repository" report. [INFO] Generating "Continuous Integration" report. [INFO] Generating "About" report. [INFO] Generating "StatSCM" report. [INFO] StatSCM - generating source code management metrics. [INFO] StatSCM Version: (1.2.0) [INFO] Configuring StatXXX [INFO] Includes: **/*.java [INFO] Excludes: **/test/**/*.java [INFO] Page title: BioJava SVN statistics [INFO] SCM Connection Type :svn [INFO] Output Directory :/home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/ [INFO] scm log > /home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/scm.log [INFO] /home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/scm.log EOF. [INFO] scm log ...; exitValue: 0 Feb 2, 2010 1:24:22 AM net.sf.statsvn.util.JavaUtilTaskLogger info INFO: Parsing SVN log '/home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/scm.log' exclude pattern '**/test/**/*.java' [ERROR] Error parsing Log file. net.sf.statcvs.input.LogSyntaxException: svn log: svn info: XML document structures must start and end within the same entity. at net.sf.statsvn.input.SvnLogfileParser.parseSvnLog(SvnLogfileParser.java:609) at net.sf.statsvn.input.SvnLogfileParser.parse(SvnLogfileParser.java:336) at net.sf.statsvn.Main.generateDefaultHTMLSuite(Main.java:278) at net.sf.statsvn.Main.generateDefaultHTMLSuite(Main.java:240) at net.sf.statscm.StatScmMojo.doSvnStats(StatScmMojo.java:255) at net.sf.statscm.StatScmMojo.executeReport(StatScmMojo.java:220) at org.apache.maven.reporting.AbstractMavenReport.generate(AbstractMavenReport.java:101) at org.apache.maven.plugins.site.ReportDocumentRenderer.renderDocument(ReportDocumentRenderer.java:139) at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.renderModule(DefaultSiteRenderer.java:269) at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.render(DefaultSiteRenderer.java:101) at org.apache.maven.plugins.site.SiteMojo.renderLocale(SiteMojo.java:133) at org.apache.maven.plugins.site.SiteMojo.execute(SiteMojo.java:100) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:556) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:535) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138) at org.apache.maven.cli.MavenCli.main(MavenCli.java:362) at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) at org.codehaus.classworlds.Launcher.main(Launcher.java:375) [ERROR] Configuration Error. org.apache.maven.reporting.MavenReportException: svn log: svn info: XML document structures must start and end within the same entity. at net.sf.statscm.StatScmMojo.doSvnStats(StatScmMojo.java:260) at net.sf.statscm.StatScmMojo.executeReport(StatScmMojo.java:220) at org.apache.maven.reporting.AbstractMavenReport.generate(AbstractMavenReport.java:101) at org.apache.maven.plugins.site.ReportDocumentRenderer.renderDocument(ReportDocumentRenderer.java:139) at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.renderModule(DefaultSiteRenderer.java:269) at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.render(DefaultSiteRenderer.java:101) at org.apache.maven.plugins.site.SiteMojo.renderLocale(SiteMojo.java:133) at org.apache.maven.plugins.site.SiteMojo.execute(SiteMojo.java:100) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:556) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:535) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138) at org.apache.maven.cli.MavenCli.main(MavenCli.java:362) at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) at org.codehaus.classworlds.Launcher.main(Launcher.java:375) [INFO] Generating "Dependencies" report. [INFO] Generating "JavaDocs" report. [WARNING] While downloading xerces:xerces:2.4.0 This artifact has been relocated to xerces:xercesImpl:2.4.0. [WARNING] While downloading jgrapht:jgrapht:0.7.3 This artifact has been relocated to org.jgrapht:jgrapht-jdk1.5:0.7.3. [WARNING] Source files encoding has not been set, using platform encoding ANSI_X3.4-1968, i.e. build is platform dependent! 81 warnings [WARNING] Javadoc Warnings [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/seq/impl/SimpleFeature.java:56: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/seq/impl/SimpleFeature.java:56: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/seq/impl/SimpleFeature.java:56: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/symbol/CrossProductAlphabetIndex.java:38: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/symbol/CrossProductAlphabetIndex.java:38: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/symbol/CrossProductAlphabetIndex.java:38: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/Annotatable.java:81: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund (docs) [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/Annotatable.java:81: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund (docs) [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/core/src/main/java/org/biojava/bio/Annotatable.java:81: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N???slund (docs) [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/SecStruc.java:402: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * 2.2-2.5 ? as "strong, mostly covalent", [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/SecStruc.java:403: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * 2.5-3.2 ? as "moderate, mostly electrostatic", [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/SecStruc.java:404: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * 3.2-4.0 ? as "weak, electrostatic". [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/gui/SequenceDisplay.java:212: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] //residueSizeSl?ider.setMinorTickSpacing(2); [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/PDBParseException.java:29: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Andreas Prlic, Thomas Down, Benjamin Schuster-B?ckler [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureException.java:29: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Andreas Prlic, Thomas Down, Benjamin Schuster-B?ckler [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/org/biojava/bio/program/das/dasalignment/DASException.java:29: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Andreas Prlic, Thomas Down, Benjamin Schuster-B?ckler [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/gui/src/main/java/org/biojava/bio/gui/sequence/GUITools.java:14: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N?slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/gui/src/main/java/org/biojava/bio/gui/sequence/RulerRenderer.java:48: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N?slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/gui/src/main/java/org/biojava/bio/gui/sequence/SymbolSequenceRenderer.java:46: warning: unmappable character for encoding ANSI_X3.4-1968 [WARNING] * @author Kalle N?slund [WARNING] ^ [WARNING] /home/andreas/src/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1351: warning - @param argument "lockVar" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/CodeContext.java:139: warning - @for.developer is an unknown tag. [WARNING] /home/andreas/src/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/CodeField.java:79: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/BigSqrt.java:137: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/BigSqrt.java:128: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:117: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:104: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/MMCIFFileReader.java:340: warning - @param argument "boolean." is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:97: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:318: warning - @param argument "boolean." is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:97: warning - @return tag cannot be used in method with void return type. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:104: warning - @param argument "isSplit" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/Group.java:154: warning - @param argument "name" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:403: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:359: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:456: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:456: warning - @param argument "chainId" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:456: warning - @param argument "range" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/org/biojava/dasobert/das/Capabilities.java:56: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/org/biojava/dasobert/das2/io/DASRegistryCoordinatesReaderXML.java:56: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Detail.java:143: warning - @return tag has no arguments. [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:178: warning - @param argument "interactors" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:187: warning - @param argument "ref" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interactor.java:237: warning - @returntrue is an unknown tag. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/Alphabet.java:44: warning - Tag @link: reference not found: SymbolEncoder#DEFAULT [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/Alphabet.java:44: warning - Tag @link: reference not found: SymbolDecoder#DEFAULT [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/AlphabetTools.java:78: warning - @param argument "syms" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:104: warning - Tag @link: missing '#': "add(int, Symbol)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:117: warning - Tag @link:illegal character: "60" in "addAll(int, Collection<? extends [WARNING] Symbol>)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:117: warning - Tag @link:illegal character: "63" in "addAll(int, Collection<? extends [WARNING] Symbol>)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:117: warning - Tag @link:illegal character: "62" in "addAll(int, Collection<? extends [WARNING] Symbol>)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:117: warning - Tag @link: missing '#': "addAll(int, Collection<? extends [WARNING] Symbol>)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:128: warning - Tag @link: missing '#': "get(int)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:139: warning - Tag @link: missing '#': "indexOf(Object)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:150: warning - Tag @link: missing '#': "lastIndexOf(Object)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:161: warning - Tag @link: missing '#': "remove(int)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolList.java:174: warning - Tag @link: missing '#': "set(int,Symbol)" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolListFormatter.java:48: warning - Tag @link: reference not found: SymbolEncoder [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolListFormatter.java:48: warning - Tag @link: reference not found: SymbolDecoder [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolListFormatter.java:126: warning - Tag @link: reference not found: SymbolEncoder [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolListFormatter.java:126: warning - Tag @link: reference not found: SymbolEncoder [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolListFormatter.java:323: warning - @param argument "is" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolMatchType.java:73: warning - Tag @link: can't find equalsIgnoreCase() in java.lang.String [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolMatchType.java:73: warning - Tag @link: can't find equalsIgnoreCase() in java.lang.String [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolMatchType.java:64: warning - Tag @link: can't find equals() in java.lang.String [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolMatchType.java:64: warning - Tag @link: can't find equals() in java.lang.String [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolMatchType.java:45: warning - Tag @link: can't find equals() in java.lang.String [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolMatchType.java:50: warning - Tag @link: can't find equalsIgnoreCase() in java.lang.String [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/TaggedSymbol.java:57: warning - @param argument "tah" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/TaggedSymbolList.java:46: warning - Tag @link: reference not found: SymbolListFormat [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/TaggedSymbolList.java:107: warning - @return tag cannot be used in method with void return type. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/TaggedSymbolList.java:123: warning - @return tag cannot be used in method with void return type. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingConverter.java:50: warning - Tag @see:illegal character: "123" in "{#setConversionRules(Properties)}" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingConverter.java:50: warning - Tag @see:illegal character: "125" in "{#setConversionRules(Properties)}" [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingConverter.java:50: warning - Tag @see: reference not found: {#setConversionRules(Properties)} [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingParser.java:43: warning - Tag @link: reference not found: Thing [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingParser.java:43: warning - Tag @link: reference not found: Thing [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingParser.java:43: warning - Tag @link: reference not found: Thing [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/io/ThingReader.java:45: warning - Tag @link: can't find canReadOne() in org.biojava3.core.io.ThingReader [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-fasta/src/main/java/org/biojava3/file/fasta/FASTA.java:105: warning - @param argument "sequence" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-blastxml/src/main/java/org/biojava3/file/blastxml/BlastXMLTools.java:114: warning - @param argument "rdr" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/symbol/SymbolListFormatter.java:126: warning - Tag @link: reference not found: SymbolEncoder [INFO] Generating "Project License" report. [INFO] Generating "Project Team" report. [INFO] Generating "Test JavaDocs" report. [WARNING] While downloading xerces:xerces:2.4.0 This artifact has been relocated to xerces:xercesImpl:2.4.0. [WARNING] While downloading jgrapht:jgrapht:0.7.3 This artifact has been relocated to org.jgrapht:jgrapht-jdk1.5:0.7.3. [WARNING] Source files encoding has not been set, using platform encoding ANSI_X3.4-1968, i.e. build is platform dependent! 63 warnings [WARNING] Javadoc Warnings [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojavax/bio/SimpleBioEntryTest.java:43: warning - @autor is an unknown tag. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojavax/SimpleCrossRefTest.java:26: warning - @autor is an unknown tag. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/utils/process/ExternalProcessTest.java:159: warning - Tag @link: reference not found: ExternalProcess#joinCommands(Object[]) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/utils/process/ExternalProcessTest.java:148: warning - Tag @link: reference not found: ExternalProcess#resolveCommands(String, Properties) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/utils/process/ExternalProcessTest.java:148: warning - Tag @link: reference not found: ExternalProcess#resolveCommands(String, Properties) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/utils/process/ExternalProcessTest.java:159: warning - Tag @link: reference not found: ExternalProcess#joinCommands(Object[]) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/molbio/RestrictionEnzymeManagerTest.java:158: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/molbio/RestrictionEnzymeManagerTest.java:168: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/molbio/RestrictionEnzymeManagerTest.java:178: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:64: warning - Tag @link: reference not found: AAindex#accessionNumber() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:71: warning - Tag @link: reference not found: AAindex#getArticleAuthors() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:101: warning - Tag @link: reference not found: AAindex#getArticleTitle() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:86: warning - Tag @link: reference not found: AAindex#getComment() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:116: warning - Tag @link: reference not found: AAindex#getDescription() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:131: warning - Tag @link: reference not found: AAindex#getJournalReference() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:146: warning - Tag @link: reference not found: AAindex#getLITDBEntryNumbers() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:78: warning - Tag @link: reference not found: AAindex#setArticleAuthors(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:108: warning - Tag @link: reference not found: AAindex#setArticleTitle(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:93: warning - Tag @link: reference not found: AAindex#setComment(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:123: warning - Tag @link: reference not found: AAindex#setDescription(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:138: warning - Tag @link: reference not found: AAindex#setJournalReference(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:153: warning - Tag @link: reference not found: AAindex#setLITDBEntryNumbers(String[]) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:161: warning - Tag @link: reference not found: AAindex#similarEntries() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:64: warning - Tag @link: reference not found: AAindex#accessionNumber() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:71: warning - Tag @link: reference not found: AAindex#getArticleAuthors() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:78: warning - Tag @link: reference not found: AAindex#setArticleAuthors(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:86: warning - Tag @link: reference not found: AAindex#getComment() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:93: warning - Tag @link: reference not found: AAindex#setComment(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:101: warning - Tag @link: reference not found: AAindex#getArticleTitle() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:108: warning - Tag @link: reference not found: AAindex#setArticleTitle(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:116: warning - Tag @link: reference not found: AAindex#getDescription() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:123: warning - Tag @link: reference not found: AAindex#setDescription(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:131: warning - Tag @link: reference not found: AAindex#getJournalReference() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:138: warning - Tag @link: reference not found: AAindex#setJournalReference(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:146: warning - Tag @link: reference not found: AAindex#getLITDBEntryNumbers() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:153: warning - Tag @link: reference not found: AAindex#setLITDBEntryNumbers(String[]) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:161: warning - Tag @link: reference not found: AAindex#similarEntries() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:96: warning - Tag @link: reference not found: SimpleSymbolPropertyTableDB#addTable(SymbolPropertyTable) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:123: warning - Tag @link: reference not found: SimpleSymbolPropertyTableDB#table(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:96: warning - Tag @link: reference not found: SimpleSymbolPropertyTableDB#addTable(SymbolPropertyTable) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:96: warning - Tag @link: reference not found: SymbolPropertyTableDB#table(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:123: warning - Tag @link: reference not found: SimpleSymbolPropertyTableDB#table(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/symbol/SymbolListTest.java:67: warning - @param argument "the" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/seq/io/LocationFormatterTest.java:99: warning - @param argument "name" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/seq/io/SmartSequenceBuilderTest.java:65: warning - @param argument "the" is not a parameter name. [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:64: warning - Tag @link: reference not found: AAindex#accessionNumber() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:96: warning - Tag @link: reference not found: SimpleSymbolPropertyTableDB#addTable(SymbolPropertyTable) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:71: warning - Tag @link: reference not found: AAindex#getArticleAuthors() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:101: warning - Tag @link: reference not found: AAindex#getArticleTitle() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:86: warning - Tag @link: reference not found: AAindex#getComment() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:116: warning - Tag @link: reference not found: AAindex#getDescription() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:131: warning - Tag @link: reference not found: AAindex#getJournalReference() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:146: warning - Tag @link: reference not found: AAindex#getLITDBEntryNumbers() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/utils/process/ExternalProcessTest.java:159: warning - Tag @link: reference not found: ExternalProcess#joinCommands(Object[]) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/utils/process/ExternalProcessTest.java:148: warning - Tag @link: reference not found: ExternalProcess#resolveCommands(String, Properties) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:78: warning - Tag @link: reference not found: AAindex#setArticleAuthors(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:108: warning - Tag @link: reference not found: AAindex#setArticleTitle(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:93: warning - Tag @link: reference not found: AAindex#setComment(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:123: warning - Tag @link: reference not found: AAindex#setDescription(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:138: warning - Tag @link: reference not found: AAindex#setJournalReference(String) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:153: warning - Tag @link: reference not found: AAindex#setLITDBEntryNumbers(String[]) [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexTest.java:161: warning - Tag @link: reference not found: AAindex#similarEntries() [WARNING] /home/andreas/src/biojava-svn/core/src/test/java/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java:123: warning - Tag @link: reference not found: SimpleSymbolPropertyTableDB#table(String) [INFO] Generating "Dependency Convergence" report. [INFO] ------------------------------------------------------------------------ [INFO] Building bytecode [INFO] task-segment: [site] [INFO] ------------------------------------------------------------------------ [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. [INFO] Preparing javadoc:test-javadoc

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[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/bytecode/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] Preparing javadoc:aggregate [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building bytecode [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building core [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building alignment [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building blast [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava structure [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building das [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-core [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-dna [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-rna [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-biosql [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-fasta [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-blastxml [INFO] ------------------------------------------------------------------------

jaxb2:generate {execution: default}

[INFO] Skipped XJC execution. Generated sources were up-to-date. [INFO] ------------------------------------------------------------------------ [INFO] Building sequencing [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building phylo [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biosql [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building gui [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] Preparing javadoc:javadoc [INFO] No goals needed for project - skipping [INFO] Preparing javadoc:test-aggregate [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building bytecode [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/bytecode/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building core [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 29 resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building alignment [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/alignment/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building blast [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 3 resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building biojava structure [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 1 resource

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building das [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/das/src/main/resources [WARNING] While downloading xerces:xerces:2.4.0 This artifact has been relocated to xerces:xercesImpl:2.4.0.

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-core [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-dna [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-dna/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-rna [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-rna/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-biosql [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-biosql/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Compiling 1 source file to /home/andreas/src/biojava-svn/sequence/sequence-biosql/target/classes [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-fasta [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-fasta/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequence-blastxml [INFO] ------------------------------------------------------------------------

jaxb2:generate {execution: default}

[INFO] Skipped XJC execution. Generated sources were up-to-date.

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 3 resources [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] Copying 0 resource [INFO] Copying 1 resource

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building sequencing [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequencing/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building phylo [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/phylo/src/main/resources [WARNING] While downloading jgrapht:jgrapht:0.7.3 This artifact has been relocated to org.jgrapht:jgrapht-jdk1.5:0.7.3.

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building biosql [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/biosql/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date [INFO] ------------------------------------------------------------------------ [INFO] Building gui [INFO] ------------------------------------------------------------------------

resources:resources {execution: default-resources}

[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/gui/src/main/resources

compiler:compile {execution: default-compile}

[INFO] Nothing to compile - all classes are up to date

site:site {execution: default-site}

[INFO] Generating "Issue Tracking" report. [INFO] Generating "Project Summary" report. [INFO] Generating "Mailing Lists" report. [INFO] Generating "Source Repository" report. [INFO] Generating "Continuous Integration" report. [INFO] Generating "About" report. [INFO] Generating "StatSCM" report. [INFO] StatSCM - generating source code management metrics. [INFO] StatSCM Version: (1.2.0) [INFO] Configuring StatXXX [INFO] Includes: **/*.java [INFO] Excludes: **/test/**/*.java [INFO] Page title: BioJava SVN statistics [INFO] SCM Connection Type :svn [INFO] Output Directory :/home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/ [INFO] scm log > /home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/scm.log [INFO] /home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/scm.log EOF. [INFO] scm log ...; exitValue: 0 Feb 2, 2010 1:29:49 AM net.sf.statsvn.util.JavaUtilTaskLogger info INFO: Parsing SVN log '/home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/scm.log' exclude pattern '**/test/**/*.java' Feb 2, 2010 1:30:18 AM net.sf.statsvn.util.JavaUtilTaskLogger info INFO: svn: Directory 'sequencing/target/.svn' containing working copy admin area is missing Feb 2, 2010 1:30:20 AM net.sf.statsvn.util.JavaUtilTaskLogger info INFO: Scheduled 0 svn diff calls on 0 threads. Feb 2, 2010 1:30:21 AM net.sf.statsvn.util.JavaUtilTaskLogger info INFO: Generating report for BioJava SVN statistics into /home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/ Feb 2, 2010 1:30:21 AM net.sf.statsvn.util.JavaUtilTaskLogger info INFO: Using default CSS file (statcvs.css) Feb 2, 2010 1:30:21 AM net.sf.statsvn.util.JavaUtilTaskLogger error SEVERE: The repository object is not valid. Please check your settings. Is the log file empty? Do you run from a checked out directory? Do you have non-committed items?

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