<?xml version="1.0" encoding="UTF-8"?>
<cruisecontrol>
  <modifications />
  <info>
    <property name="projectname" value="biojava-javadocs" />
    <property name="lastbuild" value="20100131032146" />
    <property name="lastsuccessfulbuild" value="20100131032146" />
    <property name="builddate" value="02/02/2010 01:23:24" />
    <property name="cctimestamp" value="20100202012324" />
    <property name="label" value="build.769" />
    <property name="interval" value="300" />
    <property name="lastbuildsuccessful" value="false" />
    <property name="logdir" value="/home/andreas/cruisecontrol/logs/biojava-javadocs" />
    <property name="logfile" value="log20100202012324.xml" />
  </info>
  <build error="Return code is 1" time="6 minute(s) 57 second(s)">
    <message priority="info"><![CDATA[[INFO] Scanning for projects...]]></message>
    <message priority="info"><![CDATA[[INFO] Reactor build order:]]></message>
    <message priority="info"><![CDATA[[INFO]   biojava]]></message>
    <message priority="info"><![CDATA[[INFO]   bytecode]]></message>
    <message priority="info"><![CDATA[[INFO]   core]]></message>
    <message priority="info"><![CDATA[[INFO]   alignment]]></message>
    <message priority="info"><![CDATA[[INFO]   blast]]></message>
    <message priority="info"><![CDATA[[INFO]   biojava structure]]></message>
    <message priority="info"><![CDATA[[INFO]   das]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence-core]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence-dna]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence-rna]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence-biosql]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence-fasta]]></message>
    <message priority="info"><![CDATA[[INFO]   sequence-blastxml]]></message>
    <message priority="info"><![CDATA[[INFO]   sequencing]]></message>
    <message priority="info"><![CDATA[[INFO]   phylo]]></message>
    <message priority="info"><![CDATA[[INFO]   biosql]]></message>
    <message priority="info"><![CDATA[[INFO]   gui]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building biojava]]></message>
    <message priority="info"><![CDATA[[INFO]    task-segment: [site]]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Setting property: classpath.resource.loader.class => 'org.codehaus.plexus.velocity.ContextClassLoaderResourceLoader'.]]></message>
    <message priority="info"><![CDATA[[INFO] Setting property: velocimacro.messages.on => 'false'.]]></message>
    <message priority="info"><![CDATA[[INFO] Setting property: resource.loader => 'classpath'.]]></message>
    <message priority="info"><![CDATA[[INFO] Setting property: resource.manager.logwhenfound => 'false'.]]></message>
    <message priority="info"><![CDATA[[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead.]]></message>
    <message priority="info"><![CDATA[[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead.]]></message>
    <message priority="info"><![CDATA[[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead.]]></message>
    <message priority="info"><![CDATA[[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead.]]></message>
    <message priority="info"><![CDATA[[INFO] Preparing javadoc:test-javadoc]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] Preparing javadoc:aggregate]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building biojava]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building bytecode]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building core]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building alignment]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building blast]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building biojava structure]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building das]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence-core]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence-dna]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence-rna]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence-biosql]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence-fasta]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <message priority="info"><![CDATA[[INFO] Building sequence-blastxml]]></message>
    <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    <mavengoal name="jaxb2:generate {execution: default}">
      <message priority="info"><![CDATA[Cannot find CatalogManager.properties]]></message>
      <message priority="info"><![CDATA[[INFO] Skipped XJC execution.  Generated sources were up-to-date.]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequencing]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building phylo]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building biosql]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building gui]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] Preparing javadoc:javadoc]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] Preparing javadoc:test-aggregate]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building biojava]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building bytecode]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/bytecode/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building core]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 29 resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building alignment]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/alignment/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building blast]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 3 resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building biojava structure]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 1 resource]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building das]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/das/src/main/resources]]></message>
      <message priority="info"><![CDATA[[WARNING] While downloading xerces:xerces:2.4.0]]></message>
      <message priority="info"><![CDATA[This artifact has been relocated to xerces:xercesImpl:2.4.0.]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] No goals needed for project - skipping]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence-core]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-core/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence-dna]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-dna/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence-rna]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-rna/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence-biosql]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-biosql/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Compiling 1 source file to /home/andreas/src/biojava-svn/sequence/sequence-biosql/target/classes]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence-fasta]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequence/sequence-fasta/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequence-blastxml]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="jaxb2:generate {execution: default}">
      <message priority="info"><![CDATA[[INFO] Skipped XJC execution.  Generated sources were up-to-date.]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 3 resources]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 0 resource]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 1 resource]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 0 resource]]></message>
      <message priority="info"><![CDATA[[INFO] Copying 1 resource]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building sequencing]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/sequencing/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building phylo]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/phylo/src/main/resources]]></message>
      <message priority="info"><![CDATA[[WARNING] While downloading jgrapht:jgrapht:0.7.3]]></message>
      <message priority="info"><![CDATA[This artifact has been relocated to org.jgrapht:jgrapht-jdk1.5:0.7.3.]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building biosql]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/biosql/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
      <message priority="info"><![CDATA[[INFO] Building gui]]></message>
      <message priority="info"><![CDATA[[INFO] ------------------------------------------------------------------------]]></message>
    </mavengoal>
    <mavengoal name="resources:resources {execution: default-resources}">
      <message priority="info"><![CDATA[[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[[INFO] skip non existing resourceDirectory /home/andreas/src/biojava-svn/gui/src/main/resources]]></message>
    </mavengoal>
    <mavengoal name="compiler:compile {execution: default-compile}">
      <message priority="info"><![CDATA[[INFO] Nothing to compile - all classes are up to date]]></message>
    </mavengoal>
    <mavengoal name="site:site {execution: default-site}">
      <message priority="info"><![CDATA[[INFO] Skipped "JavaDocs" report, file "apidocs/index.html" already exists for the English version.]]></message>
      <message priority="info"><![CDATA[[INFO] Skipped "Test JavaDocs" report, file "testapidocs/index.html" already exists for the English version.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Issue Tracking" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Project Summary" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Mailing Lists" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Source Repository" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Continuous Integration" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "About" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "StatSCM" report.]]></message>
      <message priority="info"><![CDATA[[INFO] StatSCM - generating source code management metrics.]]></message>
      <message priority="info"><![CDATA[[INFO] StatSCM Version: (1.2.0)]]></message>
      <message priority="info"><![CDATA[[INFO] Configuring StatXXX]]></message>
      <message priority="info"><![CDATA[[INFO] Includes: **/*.java]]></message>
      <message priority="info"><![CDATA[[INFO] Excludes: **/test/**/*.java]]></message>
      <message priority="info"><![CDATA[[INFO] Page title: BioJava SVN statistics]]></message>
      <message priority="info"><![CDATA[[INFO] SCM Connection Type :svn]]></message>
      <message priority="info"><![CDATA[[INFO] Output Directory    :/home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/]]></message>
      <message priority="info"><![CDATA[[INFO] scm log > /home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/scm.log]]></message>
      <message priority="info"><![CDATA[[INFO] /home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/scm.log EOF.]]></message>
      <message priority="info"><![CDATA[[INFO] scm log ...; exitValue: 0]]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:24:22 AM net.sf.statsvn.util.JavaUtilTaskLogger info]]></message>
      <message priority="info"><![CDATA[INFO: Parsing SVN log '/home/andreas/src/biojava-svn/target/generated-site/xdoc/statscm/scm.log' exclude pattern '**/test/**/*.java']]></message>
      <message priority="error"><![CDATA[[ERROR] Error parsing Log file.]]></message>
      <message priority="info"><![CDATA[net.sf.statcvs.input.LogSyntaxException: svn log: svn info: XML document structures must start and end within the same entity.]]></message>
      <message priority="info"><![CDATA[at net.sf.statsvn.input.SvnLogfileParser.parseSvnLog(SvnLogfileParser.java:609)]]></message>
      <message priority="info"><![CDATA[at net.sf.statsvn.input.SvnLogfileParser.parse(SvnLogfileParser.java:336)]]></message>
      <message priority="info"><![CDATA[at net.sf.statsvn.Main.generateDefaultHTMLSuite(Main.java:278)]]></message>
      <message priority="info"><![CDATA[at net.sf.statsvn.Main.generateDefaultHTMLSuite(Main.java:240)]]></message>
      <message priority="info"><![CDATA[at net.sf.statscm.StatScmMojo.doSvnStats(StatScmMojo.java:255)]]></message>
      <message priority="info"><![CDATA[at net.sf.statscm.StatScmMojo.executeReport(StatScmMojo.java:220)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.reporting.AbstractMavenReport.generate(AbstractMavenReport.java:101)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugins.site.ReportDocumentRenderer.renderDocument(ReportDocumentRenderer.java:139)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.renderModule(DefaultSiteRenderer.java:269)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.render(DefaultSiteRenderer.java:101)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugins.site.SiteMojo.renderLocale(SiteMojo.java:133)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugins.site.SiteMojo.execute(SiteMojo.java:100)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:556)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:535)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)]]></message>
      <message priority="info"><![CDATA[at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)]]></message>
      <message priority="info"><![CDATA[at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)]]></message>
      <message priority="info"><![CDATA[at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)]]></message>
      <message priority="info"><![CDATA[at java.lang.reflect.Method.invoke(Method.java:585)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.main(Launcher.java:375)]]></message>
      <message priority="error"><![CDATA[[ERROR] Configuration Error.]]></message>
      <message priority="info"><![CDATA[org.apache.maven.reporting.MavenReportException: svn log: svn info: XML document structures must start and end within the same entity.]]></message>
      <message priority="info"><![CDATA[at net.sf.statscm.StatScmMojo.doSvnStats(StatScmMojo.java:260)]]></message>
      <message priority="info"><![CDATA[at net.sf.statscm.StatScmMojo.executeReport(StatScmMojo.java:220)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.reporting.AbstractMavenReport.generate(AbstractMavenReport.java:101)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugins.site.ReportDocumentRenderer.renderDocument(ReportDocumentRenderer.java:139)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.renderModule(DefaultSiteRenderer.java:269)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.render(DefaultSiteRenderer.java:101)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugins.site.SiteMojo.renderLocale(SiteMojo.java:133)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugins.site.SiteMojo.execute(SiteMojo.java:100)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:556)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:535)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)]]></message>
      <message priority="info"><![CDATA[at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)]]></message>
      <message priority="info"><![CDATA[at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)]]></message>
      <message priority="info"><![CDATA[at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)]]></message>
      <message priority="info"><![CDATA[at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)]]></message>
      <message priority="info"><![CDATA[at java.lang.reflect.Method.invoke(Method.java:585)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)]]></message>
      <message priority="info"><![CDATA[at org.codehaus.classworlds.Launcher.main(Launcher.java:375)]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Dependencies" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "JavaDocs" report.]]></message>
      <message priority="info"><![CDATA[[WARNING] While downloading xerces:xerces:2.4.0]]></message>
      <message priority="info"><![CDATA[This artifact has been relocated to xerces:xercesImpl:2.4.0.]]></message>
      <message priority="info"><![CDATA[[WARNING] While downloading jgrapht:jgrapht:0.7.3]]></message>
      <message priority="info"><![CDATA[This artifact has been relocated to org.jgrapht:jgrapht-jdk1.5:0.7.3.]]></message>
      <message priority="info"><![CDATA[[WARNING] Source files encoding has not been set, using platform encoding ANSI_X3.4-1968, i.e. build is platform dependent!]]></message>
      <message priority="info"><![CDATA[81 warnings]]></message>
      <message priority="info"><![CDATA[[WARNING] Javadoc Warnings]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N???slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N???slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N???slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N???slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N???slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N???slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author  Kalle N???slund (docs)]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author  Kalle N???slund (docs)]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author  Kalle N???slund (docs)]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * 2.2-2.5 ? as "strong, mostly covalent",]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * 2.5-3.2 ? as "moderate, mostly electrostatic",]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * 3.2-4.0 ? as "weak, electrostatic".]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] //residueSizeSl?ider.setMinorTickSpacing(2);]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Andreas Prlic, Thomas Down, Benjamin Schuster-B?ckler]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Andreas Prlic, Thomas Down, Benjamin Schuster-B?ckler]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Andreas Prlic, Thomas Down, Benjamin Schuster-B?ckler]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N?slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N?slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] * @author Kalle N?slund]]></message>
      <message priority="info"><![CDATA[[WARNING] ^]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/CodeContext.java:139: warning - @for.developer is an unknown tag.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/CodeField.java:79: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/BigSqrt.java:137: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/secstruc/BigSqrt.java:128: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:117: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:104: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:97: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:403: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:359: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/structure/src/main/java/org/biojava/bio/structure/StructureTools.java:456: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/das/src/main/java/org/biojava/dasobert/das/Capabilities.java:56: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[WARNING] /home/andreas/src/biojava-svn/das/src/main/java/org/biojava/dasobert/das2/io/DASRegistryCoordinatesReaderXML.java:56: warning - @return tag has no arguments.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[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.]]></message>
      <message priority="info"><![CDATA[[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)"]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] Symbol>)"]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] Symbol>)"]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] Symbol>)"]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[WARNING] Symbol>)"]]></message>
      <message priority="info"><![CDATA[[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)"]]></message>
      <message priority="info"><![CDATA[[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)"]]></message>
      <message priority="info"><![CDATA[[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)"]]></message>
      <message priority="info"><![CDATA[[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)"]]></message>
      <message priority="info"><![CDATA[[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)"]]></message>
      <message priority="info"><![CDATA[[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]]></message>
      <message priority="info"><![CDATA[[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]]></message>
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    <mavengoal name="jaxb2:generate {execution: default}">
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    <mavengoal name="resources:resources {execution: default-resources}">
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    <mavengoal name="site:site {execution: default-site}">
      <message priority="info"><![CDATA[[INFO] Generating "Issue Tracking" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Project Summary" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Mailing Lists" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Source Repository" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "Continuous Integration" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "About" report.]]></message>
      <message priority="info"><![CDATA[[INFO] Generating "StatSCM" report.]]></message>
      <message priority="info"><![CDATA[[INFO] StatSCM - generating source code management metrics.]]></message>
      <message priority="info"><![CDATA[[INFO] StatSCM Version: (1.2.0)]]></message>
      <message priority="info"><![CDATA[[INFO] Configuring StatXXX]]></message>
      <message priority="info"><![CDATA[[INFO] Includes: **/*.java]]></message>
      <message priority="info"><![CDATA[[INFO] Excludes: **/test/**/*.java]]></message>
      <message priority="info"><![CDATA[[INFO] Page title: BioJava SVN statistics]]></message>
      <message priority="info"><![CDATA[[INFO] SCM Connection Type :svn]]></message>
      <message priority="info"><![CDATA[[INFO] Output Directory    :/home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/]]></message>
      <message priority="info"><![CDATA[[INFO] scm log > /home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/scm.log]]></message>
      <message priority="info"><![CDATA[[INFO] /home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/scm.log EOF.]]></message>
      <message priority="info"><![CDATA[[INFO] scm log ...; exitValue: 0]]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:29:49 AM net.sf.statsvn.util.JavaUtilTaskLogger info]]></message>
      <message priority="info"><![CDATA[INFO: Parsing SVN log '/home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/scm.log' exclude pattern '**/test/**/*.java']]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:30:18 AM net.sf.statsvn.util.JavaUtilTaskLogger info]]></message>
      <message priority="info"><![CDATA[INFO: svn: Directory 'sequencing/target/.svn' containing working copy admin area is missing]]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:30:20 AM net.sf.statsvn.util.JavaUtilTaskLogger info]]></message>
      <message priority="info"><![CDATA[INFO: Scheduled 0 svn diff calls on 0 threads.]]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:30:21 AM net.sf.statsvn.util.JavaUtilTaskLogger info]]></message>
      <message priority="info"><![CDATA[INFO: Generating report for BioJava SVN statistics into /home/andreas/src/biojava-svn/bytecode/target/generated-site/xdoc/statscm/]]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:30:21 AM net.sf.statsvn.util.JavaUtilTaskLogger info]]></message>
      <message priority="info"><![CDATA[INFO: Using default CSS file (statcvs.css)]]></message>
      <message priority="info"><![CDATA[Feb 2, 2010 1:30:21 AM net.sf.statsvn.util.JavaUtilTaskLogger error]]></message>
      <message priority="info"><![CDATA[SEVERE: The repository object is not valid. Please check your settings.]]></message>
      <message priority="info"><![CDATA[Is the log file empty? Do you run from a checked out directory? Do you have non-committed items?]]></message>
    </mavengoal>
  </build>
</cruisecontrol>

