Project
 
now building since
02/02/2010 01:35:36
 
Latest Build
02/02/2010 01:23:24
02/02/2010 01:10:47
02/02/2010 00:56:48
02/02/2010 00:45:34
02/02/2010 00:33:38
02/02/2010 00:22:03
02/02/2010 00:09:52
02/01/2010 23:56:10
02/01/2010 23:43:55
02/01/2010 23:31:39
 

 
BUILD FAILED
Ant Error Message: Return code is 1
Date of build: 02/02/2010 01:23:24
Time to build: 6 minute(s) 57 second(s)

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
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[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]
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[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
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] Preparing javadoc:aggregate
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[INFO] Building biojava
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[INFO] Building bytecode
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[INFO] Building core
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[INFO] Building alignment
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[INFO] No goals needed for project - skipping
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[INFO] Building blast
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[INFO] No goals needed for project - skipping
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[INFO] Building biojava structure
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[INFO] Building das
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[INFO] Building sequence
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[INFO] Building sequence-core
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[INFO] Building sequence-dna
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[INFO] Building sequence-rna
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[INFO] Building sequence-biosql
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[INFO] Building sequence-fasta
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[INFO] Building sequence-blastxml
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jaxb2:generate {execution: default}
[INFO] Skipped XJC execution. Generated sources were up-to-date.
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[INFO] Building sequencing
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[INFO] Building phylo
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[INFO] No goals needed for project - skipping
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[INFO] Building biosql
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[INFO] No goals needed for project - skipping
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[INFO] Building gui
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[INFO] No goals needed for project - skipping
[INFO] Preparing javadoc:javadoc
[INFO] No goals needed for project - skipping
[INFO] Preparing javadoc:test-aggregate
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[INFO] Building biojava
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[INFO] No goals needed for project - skipping
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[INFO] Building bytecode
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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
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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
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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
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[INFO] Building blast
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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
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[INFO] Building das
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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
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[INFO] Building sequence
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[INFO] No goals needed for project - skipping
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[INFO] Building sequence-core
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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
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[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?

 Unit Tests: (0)
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