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View results here -> <a href="http://emmy.rcsb.org:8080/cruisecontrol/buildresults/biojava-svn?log=log20100728164837Lbuild.35">http://emmy.rcsb.org:8080/cruisecontrol/buildresults/biojava-svn?log=log20100728164837Lbuild.35</a><p>
<table xmlns:lxslt="http://xml.apache.org/xslt" align="center" cellpadding="2" cellspacing="0" border="0" class="header" width="98%">
<tr>
<th class="big" colspan="2">BUILD COMPLETE -
build.35
</th>
</tr>
<tr>
<th>Date of build:</th>
<td>2010-07-28T23:48:37</td>
</tr>
<tr>
<th>Time to build:</th>
<td>48 minute(s) 55 second(s)</td>
</tr>
<tr>
<th>Last changed:</th>
<td>2010-07-28T23:05:27</td>
</tr>
<tr>
<th>Last log entry:</th>
<td>improvements to memory usage during multiple sequence alignment</td>
</tr>
</table><p>
<p>
<table xmlns="http://www.w3.org/TR/html4/strict.dtd" align="center" cellpadding="2" cellspacing="0" border="0" width="98%">
<tr class="compile-sectionheader">
<td>Initial Messages</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Scanning for projects...<br/></span><span class="compile-data">[INFO] Reactor build order: <br/></span><span class="compile-data">[INFO] biojava<br/></span><span class="compile-data">[INFO] bytecode<br/></span><span class="compile-data">[INFO] core<br/></span><span class="compile-data">[INFO] alignment<br/></span><span class="compile-data">[INFO] blast<br/></span><span class="compile-data">[INFO] biojava3-structure<br/></span><span class="compile-data">[INFO] das<br/></span><span class="compile-data">[INFO] sequence<br/></span><span class="compile-data">[INFO] sequence-core<br/></span><span class="compile-data">[INFO] sequence-rna<br/></span><span class="compile-data">[INFO] sequence-biosql<br/></span><span class="compile-data">[INFO] sequence-fasta<br/></span><span class="compile-data">[INFO] sequence-blastxml<br/></span><span class="compile-data">[INFO] sequencing<br/></span><span class="compile-data">[INFO] phylo<br/></span><span class="compile-data">[INFO] biosql<br/></span><span class="compile-data">[INFO] gui<br/></span><span class="compile-data">[INFO] biojava3-core<br/></span><span class="compile-data">[INFO] biojava3-phylo<br/></span><span class="compile-data">[INFO] biojava3-structure-gui<br/></span><span class="compile-data">[INFO] biojava3-alignment<br/></span><span class="compile-data">[INFO] biojava3-genome<br/></span><span class="compile-data">[INFO] biojava3-protmod<br/></span><span class="compile-data">[INFO] biojava3-ws<br/></span><span class="compile-data">[INFO] Searching repository for plugin with prefix: 'source'.<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>site:attach-descriptor {execution: default-attach-descriptor}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava/3.0-SNAPSHOT/biojava-3.0-SNAPSHOT.pom<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Not executing Javadoc as the project is not a Java classpath-capable package<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>site:attach-descriptor {execution: default-attach-descriptor}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava/3.0-SNAPSHOT/biojava-3.0-SNAPSHOT.pom<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava/3.0-SNAPSHOT/biojava-3.0-SNAPSHOT.pom<br/></span><span class="compile-data">7K uploaded (biojava-3.0-SNAPSHOT.pom)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava'<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building bytecode<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/bytecode/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/bytecode/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 44 source files to /opt/cruise/projects/biojava-svn/bytecode/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/bytecode/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">3 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1351: warning -
@param argument "lockVar" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/CodeContext.java:139: warning
- @for.developer is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/bytecode/src/main/java/org/biojava/utils/bytecode/CodeField.java:79: warning -
@return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/bytecode/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/bytecode/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/bytecode/target/bytecode-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">94K uploaded (bytecode-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:bytecode:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:bytecode'<br/></span><span class="compile-data">[INFO] Uploading project information for bytecode 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">59K uploaded (bytecode-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/3.0-SNAPSHOT/bytecode-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">250K uploaded (bytecode-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building core<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/core/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 29 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1067 source files to /opt/cruise/projects/biojava-svn/core/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 50 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 145 source files to /opt/cruise/projects/biojava-svn/core/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.utils.lsid.LifeScienceIdentifierTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolListTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.042 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefAuthorTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetExtendedName<br/></span><span class="compile-data">testIsConsortium<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.EmissionStateEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SeqContentPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.EmptyRichAnnotationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureFilterTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2255Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefTest<br/></span><span class="compile-data">testGetLocation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetRemark<br/></span><span class="compile-data">testSetCrossref<br/></span><span class="compile-data">testGetAuthors<br/></span><span class="compile-data">testGetAuthorList<br/></span><span class="compile-data">testGetCRC<br/></span><span class="compile-data">testGetRemark<br/></span><span class="compile-data">testGetCrossref<br/></span><span class="compile-data">testGetTitle<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SmartSequenceBuilderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.382 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest<br/></span><span class="compile-data">java.lang.NullPointerException: table is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">java.lang.NullPointerException: name is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">org.biojava.bio.seq.db.IllegalIDException: No table found with name test.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.filter.FilterTransformerTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableOntologyTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testContainsTerm<br/></span><span class="compile-data">testGetOrCreateTerm<br/></span><span class="compile-data">testGetOrImportTerm<br/></span><span class="compile-data">testCreateTerm<br/></span><span class="compile-data">testImportTerm<br/></span><span class="compile-data">testCreateTriple<br/></span><span class="compile-data">testDeleteTerm<br/></span><span class="compile-data">testGetTriples<br/></span><span class="compile-data">testSetTripleSet<br/></span><span class="compile-data">testGetTripleSet<br/></span><span class="compile-data">testGetTerms<br/></span><span class="compile-data">testSetTermSet<br/></span><span class="compile-data">testGetTermSet<br/></span><span class="compile-data">testContainsTriple<br/></span><span class="compile-data">testCreateVariable<br/></span><span class="compile-data">testGetOps<br/></span><span class="compile-data">Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.indexdb.IndexToolsTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.ProteinToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.bio.SimpleBioEntryTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetTaxon<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetComments<br/></span><span class="compile-data">testGetRankedDocRefs<br/></span><span class="compile-data">testGetRelationships<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testSetDivision<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetDivision<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testGetNamespace<br/></span><span class="compile-data">testGetTaxon<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testAddRankedDocRef<br/></span><span class="compile-data">testRemoveRankedDocRef<br/></span><span class="compile-data">testAddComment<br/></span><span class="compile-data">testRemoveComment<br/></span><span class="compile-data">testAddRelationship<br/></span><span class="compile-data">testRemoveRelationship<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRichAnnotationTest<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">testGetPropertys<br/></span><span class="compile-data">testRemoveProperty2<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.PointLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.MergeAnnotationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.DPSerializationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SymbolListCharSequenceTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CodonPrefToolsTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.LocationFormatterTest<br/></span><span class="compile-data">Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.179 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2249_2248Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerFactoryTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCrossRefTest<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testGetDbname<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.DoubleAlphabetTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSequenceTest<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TestSoftMaskedAlphabet<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IntegerAlphabetTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.EMBLFormatTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerTest<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature))<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec<br/></span><span class="compile-data">Running org.biojava.utils.RepeatedCharSequenceTest<br/></span><span class="compile-data">JAM<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FilterUtilsTest<br/></span><span class="compile-data">Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedDocRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetDocumentReference<br/></span><span class="compile-data">testGetStart<br/></span><span class="compile-data">testGetEnd<br/></span><span class="compile-data">testSetLocation<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.RichLocationToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSeqSerializationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.PatternCheckerTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MergeLocationTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTermTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetObsolete<br/></span><span class="compile-data">testSetObsolete<br/></span><span class="compile-data">Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.utils.ListToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.HashSequenceDBTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TranslationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNamespaceTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetAcronym<br/></span><span class="compile-data">testSetAuthority<br/></span><span class="compile-data">testSetURI<br/></span><span class="compile-data">testGetAcronym<br/></span><span class="compile-data">testGetAuthority<br/></span><span class="compile-data">testGetURI<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.DummyCrossReferenceResolverTest<br/></span><span class="compile-data">testGetRemoteSymbolList<br/></span><span class="compile-data">testGetRemoteBioEntry<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.AnnotationTypeTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.RNAToolsTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.directory.SystemRegistryTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SeqSerializationTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.NewSimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.MaxMismatchPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.filterxml.FilterXMLTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CompoundLocationTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.ProportionalSelectionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CircularLocationTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureHolderUtilsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.IsoelectricPointCalcTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetManagerTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.CompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductTokenizationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetSerializationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaUriParserTest<br/></span><span class="compile-data">oneName<br/></span><span class="compile-data">:trail<br/></span><span class="compile-data">lead:<br/></span><span class="compile-data">urn:obda.org:format:embl/ac<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaInitialContextFactoryTest<br/></span><span class="compile-data">lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@638e8fbd}<br/></span><span class="compile-data">My component is urn:open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@adc9515}<br/></span><span class="compile-data">My component is open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@17bf9b45, format=org.biojava.naming.ObdaContext@246adb31, alphabet=org.biojava.naming.ObdaContext@635c80a4}<br/></span><span class="compile-data">My component is format:embl<br/></span><span class="compile-data">lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@4e01c1f2, genbank=org.biojava.naming.ObdaContext@55641ee0, swissprot=org.biojava.naming.ObdaContext@20272fec,
embl=org.biojava.naming.ObdaContext@6cbb3f71}<br/></span><span class="compile-data">My component is embl<br/></span><span class="compile-data">Reached <br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: urn -> org.biojava.naming.ObdaContext@44755866<br/></span><span class="compile-data">Reached urn<br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: open-bio.org -> org.biojava.naming.ObdaContext@73feb3a6<br/></span><span class="compile-data">Reached urn:open-bio.org<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed<br/></span><span class="compile-data">by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the<br/></span><span class="compile-data">module obda-specs in the cvs repository located at<br/></span><span class="compile-data">pub.open-bio.org:/home/repository/obf-common.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@380b4f9<br/></span><span class="compile-data">Reached urn:open-bio.org:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The namespace for URNs that identify data types. It is expected that the types<br/></span><span class="compile-data">that are given IDs will be very general in nature, such as Sequence and<br/></span><span class="compile-data">File Format. All types are of type urn:open-bio.org:type:type. Any URN in the<br/></span><span class="compile-data">type namespace that is not of this type is not conforming to the OBDA<br/></span><span class="compile-data">specification for this namespace.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@76e9493a<br/></span><span class="compile-data">Reached urn:open-bio.org:type:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The OBDA URN that identifies the concept of 'type'. In a given language, this<br/></span><span class="compile-data">may map to the types of data structures, or objects. Alternativel, it may<br/></span><span class="compile-data">map to a particular set of keys being present in a map, or a term in an<br/></span><span class="compile-data">ontology. This is not important. The important thing is that we have unique<br/></span><span class="compile-data">identifiers for common types that all projects use and interact with.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@4dc6bbd3<br/></span><span class="compile-data">Reached urn:open-bio.org:type:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A file format. Many file formats are used in bioinformatics. Entities of this<br/></span><span class="compile-data">type identify a format. The format can be used to choose how to treat a file.<br/></span><span class="compile-data">The format is not expected to be resolvable to a formal deffinition of the<br/></span><span class="compile-data">file structure using OBDA-supplied functionality. Different applications may<br/></span><span class="compile-data">chose to process a stream with the same format URN in different ways. This<br/></span><span class="compile-data">type of URN is purely there to identify the format of the stream, not the<br/></span><span class="compile-data">manner in which it should be processed.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@32554189<br/></span><span class="compile-data">Reached urn:open-bio.org:type:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A biological sequence alphabet. Biological sequences are often represented as<br/></span><span class="compile-data">strings of characters. However, in differnt circumstances, the same characters<br/></span><span class="compile-data">can represent different things. For example, in DNA, the 't' character<br/></span><span class="compile-data">represents tyrosine. In Protein, this same character represents tryptophan.<br/></span><span class="compile-data">Associating alphabets with these sequences disambiguates their interpretation.<br/></span><span class="compile-data">Alphabets do not define a mapping to or from strings, but should be used<br/></span><span class="compile-data">wherever the type of the content of a sequence needs to be stated.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@7b41a32f<br/></span><span class="compile-data">Reached urn:open-bio.org:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace for OBDA URNs that define formats. All URNs within this namespace<br/></span><span class="compile-data">must be of the type urn:open-bio.org:type:format. Any URN in this namespace that<br/></span><span class="compile-data">is not of that type is not a valid OBDA URN.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: enzyme -> org.biojava.naming.ObdaContext@1240a1e1<br/></span><span class="compile-data">Reached urn:open-bio.org:format:enzyme<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The Enzyme database entry format. The enzyme database can be downloaded from<br/></span><span class="compile-data">the ebi at:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/<br/></span><span class="compile-data">For an example of a file in this format, see:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat<br/></span><span class="compile-data">The format is described more fully in<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: genbank -> org.biojava.naming.ObdaContext@5143c423<br/></span><span class="compile-data">Reached urn:open-bio.org:format:genbank<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The GENBANK file format associated with the GENBANK sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: swissprot -> org.biojava.naming.ObdaContext@3801ff83<br/></span><span class="compile-data">Reached urn:open-bio.org:format:swissprot<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The SWISSPROT file format as used in the SWISSPROT sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: embl -> org.biojava.naming.ObdaContext@b2e0e2f<br/></span><span class="compile-data">Reached urn:open-bio.org:format:embl<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The EMBL file format associated with entries in the EMBL sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@7ca53564<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace within which to store alphabet identifiers. Alphabets should<br/></span><span class="compile-data">represent URNs that represent objects of the type identified by<br/></span><span class="compile-data">urn:open-bio.org:type:alphabet, and any useage outside of this is not supported.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: rna -> org.biojava.naming.ObdaContext@4254782a<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:rna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and u. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: protein -> org.biojava.naming.ObdaContext@379d2f6b<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:protein<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The protein alphabet. Proteins are composed from amino-acids. To find out more,<br/></span><span class="compile-data">read a biochemistry or genetics text book. It is common for protein sequences<br/></span><span class="compile-data">to be represented by characters, but this is not a formal requirement for<br/></span><span class="compile-data">a resource to publish an alphabet equal to this identifier.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: dna -> org.biojava.naming.ObdaContext@30943653<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:dna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and t. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.GappedSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.UkkonenSuffixTreeTest<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.WeightedSetTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleWobbleDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNoteTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testSetTerm<br/></span><span class="compile-data">testGetValue<br/></span><span class="compile-data">testSetValue<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.utils.SmallMapTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.TranslatedDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichFeatureTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.RangeLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.directory.OBDARegistryParserTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.169 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TripleImplTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MotifToolsTest<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.RegexTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.CircularSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.DNAToolsTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolSerializationTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.TestHashSequenceDB<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.GenbankFormatTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.MassCalcTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.MarkovModelEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionToolsTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.LinearAlphabetIndexTest<br/></span><span class="compile-data">getAlphabet<br/></span><span class="compile-data">symbolForIndex<br/></span><span class="compile-data">indexForSymbol<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleCodonPrefTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTripleTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetSubject<br/></span><span class="compile-data">testGetObject<br/></span><span class="compile-data">testGetPredicate<br/></span><span class="compile-data">testAddDescriptor<br/></span><span class="compile-data">testRemoveDescriptor<br/></span><span class="compile-data">testGetDescriptors<br/></span><span class="compile-data">testSetDescriptors<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.INSDseqFormatTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.phred.PhredToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.UniProtFormatTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.SubSequenceTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.NameTokenizationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest<br/></span><span class="compile-data">testSetName<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetNameClass<br/></span><span class="compile-data">testGetNameClass<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCommentTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetComment<br/></span><span class="compile-data">testSetComment<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.MergeFeatureHolderTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.utils.process.ExternalProcessTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedCrossRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetCrossRef<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SeqIOToolsTest<br/></span><span class="compile-data">idb length: 79<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.464 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistSerTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.GappedSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2250_2256Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 sec<br/></span><span class="compile-data">Running org.biojavax.CrossReferenceResolutionExceptionTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.ontology.ParseOBOFileTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.339 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.BetweenLocationTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TermImplTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimplePopulationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IndexedNoAmbPackTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.ontology.OntologyTest<br/></span><span class="compile-data">Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.utils.automata.NfaTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.directory.RegistryConfigurationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimpleOrganismTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.GAToolsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexTest<br/></span><span class="compile-data">org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:326)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data">Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.MSFAlignmentFormatTest<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 876, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">2 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/core/src/main/java/org/biojava/bio/alignment/SimpleAlignment.java:303: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/core/src/main/java/org/biojavax/RichObjectFactory.java:74: warning - Tag @see:
reference not found: org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 29 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 50 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.utils.lsid.LifeScienceIdentifierTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolListTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.045 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefAuthorTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetExtendedName<br/></span><span class="compile-data">testIsConsortium<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.EmissionStateEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SeqContentPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.EmptyRichAnnotationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureFilterTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2255Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefTest<br/></span><span class="compile-data">testGetLocation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetRemark<br/></span><span class="compile-data">testSetCrossref<br/></span><span class="compile-data">testGetAuthors<br/></span><span class="compile-data">testGetAuthorList<br/></span><span class="compile-data">testGetCRC<br/></span><span class="compile-data">testGetRemark<br/></span><span class="compile-data">testGetCrossref<br/></span><span class="compile-data">testGetTitle<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SmartSequenceBuilderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.392 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest<br/></span><span class="compile-data">java.lang.NullPointerException: table is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">java.lang.NullPointerException: name is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">org.biojava.bio.seq.db.IllegalIDException: No table found with name test.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.filter.FilterTransformerTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableOntologyTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testContainsTerm<br/></span><span class="compile-data">testGetOrCreateTerm<br/></span><span class="compile-data">testGetOrImportTerm<br/></span><span class="compile-data">testCreateTerm<br/></span><span class="compile-data">testImportTerm<br/></span><span class="compile-data">testCreateTriple<br/></span><span class="compile-data">testDeleteTerm<br/></span><span class="compile-data">testGetTriples<br/></span><span class="compile-data">testSetTripleSet<br/></span><span class="compile-data">testGetTripleSet<br/></span><span class="compile-data">testGetTerms<br/></span><span class="compile-data">testSetTermSet<br/></span><span class="compile-data">testGetTermSet<br/></span><span class="compile-data">testContainsTriple<br/></span><span class="compile-data">testCreateVariable<br/></span><span class="compile-data">testGetOps<br/></span><span class="compile-data">Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.indexdb.IndexToolsTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.ProteinToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.bio.SimpleBioEntryTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetTaxon<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetComments<br/></span><span class="compile-data">testGetRankedDocRefs<br/></span><span class="compile-data">testGetRelationships<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testSetDivision<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetDivision<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testGetNamespace<br/></span><span class="compile-data">testGetTaxon<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testAddRankedDocRef<br/></span><span class="compile-data">testRemoveRankedDocRef<br/></span><span class="compile-data">testAddComment<br/></span><span class="compile-data">testRemoveComment<br/></span><span class="compile-data">testAddRelationship<br/></span><span class="compile-data">testRemoveRelationship<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRichAnnotationTest<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">testGetPropertys<br/></span><span class="compile-data">testRemoveProperty2<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.PointLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.MergeAnnotationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.DPSerializationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SymbolListCharSequenceTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CodonPrefToolsTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.LocationFormatterTest<br/></span><span class="compile-data">Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2249_2248Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerFactoryTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCrossRefTest<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testGetDbname<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.DoubleAlphabetTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSequenceTest<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TestSoftMaskedAlphabet<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IntegerAlphabetTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.EMBLFormatTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerTest<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature))<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.utils.RepeatedCharSequenceTest<br/></span><span class="compile-data">JAM<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FilterUtilsTest<br/></span><span class="compile-data">Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedDocRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetDocumentReference<br/></span><span class="compile-data">testGetStart<br/></span><span class="compile-data">testGetEnd<br/></span><span class="compile-data">testSetLocation<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.RichLocationToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSeqSerializationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.PatternCheckerTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MergeLocationTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTermTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetObsolete<br/></span><span class="compile-data">testSetObsolete<br/></span><span class="compile-data">Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.utils.ListToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.HashSequenceDBTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TranslationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNamespaceTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetAcronym<br/></span><span class="compile-data">testSetAuthority<br/></span><span class="compile-data">testSetURI<br/></span><span class="compile-data">testGetAcronym<br/></span><span class="compile-data">testGetAuthority<br/></span><span class="compile-data">testGetURI<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.DummyCrossReferenceResolverTest<br/></span><span class="compile-data">testGetRemoteSymbolList<br/></span><span class="compile-data">testGetRemoteBioEntry<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.AnnotationTypeTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.RNAToolsTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.directory.SystemRegistryTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SeqSerializationTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.NewSimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.MaxMismatchPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.filterxml.FilterXMLTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CompoundLocationTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.ProportionalSelectionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CircularLocationTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureHolderUtilsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.IsoelectricPointCalcTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetManagerTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.CompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductTokenizationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetSerializationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaUriParserTest<br/></span><span class="compile-data">oneName<br/></span><span class="compile-data">:trail<br/></span><span class="compile-data">lead:<br/></span><span class="compile-data">urn:obda.org:format:embl/ac<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaInitialContextFactoryTest<br/></span><span class="compile-data">lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@635c80a4}<br/></span><span class="compile-data">My component is urn:open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@55641ee0}<br/></span><span class="compile-data">My component is open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@20272fec, format=org.biojava.naming.ObdaContext@6cbb3f71, alphabet=org.biojava.naming.ObdaContext@79424b7b}<br/></span><span class="compile-data">My component is format:embl<br/></span><span class="compile-data">lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@6f69b66e, genbank=org.biojava.naming.ObdaContext@54828e7, swissprot=org.biojava.naming.ObdaContext@44755866,
embl=org.biojava.naming.ObdaContext@73feb3a6}<br/></span><span class="compile-data">My component is embl<br/></span><span class="compile-data">Reached <br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: urn -> org.biojava.naming.ObdaContext@4dc6bbd3<br/></span><span class="compile-data">Reached urn<br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: open-bio.org -> org.biojava.naming.ObdaContext@32554189<br/></span><span class="compile-data">Reached urn:open-bio.org<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed<br/></span><span class="compile-data">by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the<br/></span><span class="compile-data">module obda-specs in the cvs repository located at<br/></span><span class="compile-data">pub.open-bio.org:/home/repository/obf-common.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@1240a1e1<br/></span><span class="compile-data">Reached urn:open-bio.org:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The namespace for URNs that identify data types. It is expected that the types<br/></span><span class="compile-data">that are given IDs will be very general in nature, such as Sequence and<br/></span><span class="compile-data">File Format. All types are of type urn:open-bio.org:type:type. Any URN in the<br/></span><span class="compile-data">type namespace that is not of this type is not conforming to the OBDA<br/></span><span class="compile-data">specification for this namespace.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@5143c423<br/></span><span class="compile-data">Reached urn:open-bio.org:type:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The OBDA URN that identifies the concept of 'type'. In a given language, this<br/></span><span class="compile-data">may map to the types of data structures, or objects. Alternativel, it may<br/></span><span class="compile-data">map to a particular set of keys being present in a map, or a term in an<br/></span><span class="compile-data">ontology. This is not important. The important thing is that we have unique<br/></span><span class="compile-data">identifiers for common types that all projects use and interact with.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@3801ff83<br/></span><span class="compile-data">Reached urn:open-bio.org:type:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A file format. Many file formats are used in bioinformatics. Entities of this<br/></span><span class="compile-data">type identify a format. The format can be used to choose how to treat a file.<br/></span><span class="compile-data">The format is not expected to be resolvable to a formal deffinition of the<br/></span><span class="compile-data">file structure using OBDA-supplied functionality. Different applications may<br/></span><span class="compile-data">chose to process a stream with the same format URN in different ways. This<br/></span><span class="compile-data">type of URN is purely there to identify the format of the stream, not the<br/></span><span class="compile-data">manner in which it should be processed.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@b2e0e2f<br/></span><span class="compile-data">Reached urn:open-bio.org:type:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A biological sequence alphabet. Biological sequences are often represented as<br/></span><span class="compile-data">strings of characters. However, in differnt circumstances, the same characters<br/></span><span class="compile-data">can represent different things. For example, in DNA, the 't' character<br/></span><span class="compile-data">represents tyrosine. In Protein, this same character represents tryptophan.<br/></span><span class="compile-data">Associating alphabets with these sequences disambiguates their interpretation.<br/></span><span class="compile-data">Alphabets do not define a mapping to or from strings, but should be used<br/></span><span class="compile-data">wherever the type of the content of a sequence needs to be stated.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@7ca53564<br/></span><span class="compile-data">Reached urn:open-bio.org:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace for OBDA URNs that define formats. All URNs within this namespace<br/></span><span class="compile-data">must be of the type urn:open-bio.org:type:format. Any URN in this namespace that<br/></span><span class="compile-data">is not of that type is not a valid OBDA URN.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: enzyme -> org.biojava.naming.ObdaContext@4254782a<br/></span><span class="compile-data">Reached urn:open-bio.org:format:enzyme<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The Enzyme database entry format. The enzyme database can be downloaded from<br/></span><span class="compile-data">the ebi at:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/<br/></span><span class="compile-data">For an example of a file in this format, see:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat<br/></span><span class="compile-data">The format is described more fully in<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: genbank -> org.biojava.naming.ObdaContext@379d2f6b<br/></span><span class="compile-data">Reached urn:open-bio.org:format:genbank<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The GENBANK file format associated with the GENBANK sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: swissprot -> org.biojava.naming.ObdaContext@30943653<br/></span><span class="compile-data">Reached urn:open-bio.org:format:swissprot<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The SWISSPROT file format as used in the SWISSPROT sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: embl -> org.biojava.naming.ObdaContext@527a9c0f<br/></span><span class="compile-data">Reached urn:open-bio.org:format:embl<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The EMBL file format associated with entries in the EMBL sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@6f9bc716<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace within which to store alphabet identifiers. Alphabets should<br/></span><span class="compile-data">represent URNs that represent objects of the type identified by<br/></span><span class="compile-data">urn:open-bio.org:type:alphabet, and any useage outside of this is not supported.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: rna -> org.biojava.naming.ObdaContext@5c2bae98<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:rna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and u. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: protein -> org.biojava.naming.ObdaContext@37d3ac6e<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:protein<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The protein alphabet. Proteins are composed from amino-acids. To find out more,<br/></span><span class="compile-data">read a biochemistry or genetics text book. It is common for protein sequences<br/></span><span class="compile-data">to be represented by characters, but this is not a formal requirement for<br/></span><span class="compile-data">a resource to publish an alphabet equal to this identifier.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: dna -> org.biojava.naming.ObdaContext@29dd8664<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:dna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and t. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.GappedSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.UkkonenSuffixTreeTest<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.WeightedSetTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleWobbleDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNoteTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testSetTerm<br/></span><span class="compile-data">testGetValue<br/></span><span class="compile-data">testSetValue<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.utils.SmallMapTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.TranslatedDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichFeatureTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.RangeLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.directory.OBDARegistryParserTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.171 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TripleImplTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MotifToolsTest<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.RegexTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.CircularSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.DNAToolsTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolSerializationTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.TestHashSequenceDB<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.GenbankFormatTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.MassCalcTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.MarkovModelEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionToolsTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.LinearAlphabetIndexTest<br/></span><span class="compile-data">getAlphabet<br/></span><span class="compile-data">symbolForIndex<br/></span><span class="compile-data">indexForSymbol<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleCodonPrefTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTripleTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetSubject<br/></span><span class="compile-data">testGetObject<br/></span><span class="compile-data">testGetPredicate<br/></span><span class="compile-data">testAddDescriptor<br/></span><span class="compile-data">testRemoveDescriptor<br/></span><span class="compile-data">testGetDescriptors<br/></span><span class="compile-data">testSetDescriptors<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.INSDseqFormatTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.phred.PhredToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.UniProtFormatTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.SubSequenceTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.NameTokenizationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest<br/></span><span class="compile-data">testSetName<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetNameClass<br/></span><span class="compile-data">testGetNameClass<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCommentTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetComment<br/></span><span class="compile-data">testSetComment<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.MergeFeatureHolderTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.utils.process.ExternalProcessTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.218 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedCrossRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetCrossRef<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SeqIOToolsTest<br/></span><span class="compile-data">idb length: 79<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.436 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistSerTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.GappedSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2250_2256Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 sec<br/></span><span class="compile-data">Running org.biojavax.CrossReferenceResolutionExceptionTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.ontology.ParseOBOFileTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.348 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.BetweenLocationTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TermImplTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimplePopulationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IndexedNoAmbPackTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.ontology.OntologyTest<br/></span><span class="compile-data">Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava.utils.automata.NfaTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.directory.RegistryConfigurationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimpleOrganismTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.GAToolsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexTest<br/></span><span class="compile-data">org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:326)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.MSFAlignmentFormatTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 876, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/core/target/core-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">2418K uploaded (core-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:core:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:core'<br/></span><span class="compile-data">[INFO] Uploading project information for core 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">2043K uploaded (core-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/3.0-SNAPSHOT/core-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">13178K uploaded (core-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building alignment<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/alignment/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/alignment/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 14 source files to /opt/cruise/projects/biojava-svn/alignment/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 3 source files to /opt/cruise/projects/biojava-svn/alignment/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/alignment/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.alignment.SubstitutionMatrixTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec<br/></span><span class="compile-data">Running org.biojava.bio.alignment.FlexibleAlignmentTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">13 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AbstractULAlignment.java:207:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:57: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:391: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:526: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:518: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:326: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:334: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:342: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:350: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:358: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:366: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:226: warning
- @param argument "queryLength" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/alignment/src/main/java/org/biojava/bio/alignment/FlexibleAlignment.java:270: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/alignment/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/alignment/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.alignment.SubstitutionMatrixTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.215 sec<br/></span><span class="compile-data">Running org.biojava.bio.alignment.FlexibleAlignmentTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.282 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/alignment/target/alignment-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">36K uploaded (alignment-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:alignment:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:alignment'<br/></span><span class="compile-data">[INFO] Uploading project information for alignment 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">33K uploaded (alignment-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/3.0-SNAPSHOT/alignment-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">198K uploaded (alignment-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building blast<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/blast/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 56 source files to /opt/cruise/projects/biojava-svn/blast/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 22 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 19 source files to /opt/cruise/projects/biojava-svn/blast/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/blast/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.506 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.251 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.332 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.518 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.805 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.297 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.647 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.BlastTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.78 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.blastxml.BlastXMLTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.722 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.667 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.313 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.777 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 118, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 22 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/blast/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.509 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.17 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.259 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.48 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.798 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.295 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.644 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.329 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.BlastTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.784 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.blastxml.BlastXMLTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.669 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.318 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.774 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 118, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/blast/target/blast-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">181K uploaded (blast-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Uploading project information for blast 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:blast:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:blast'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">128K uploaded (blast-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/3.0-SNAPSHOT/blast-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">300K uploaded (blast-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-structure<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/structure/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 189 source files to /opt/cruise/projects/biojava-svn/structure/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
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<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 34 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 44 source files to /opt/cruise/projects/biojava-svn/structure/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/structure/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructureTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.726 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.benchmark.MultipleAlignmentTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.643 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructurePairAlignerTest<br/></span><span class="compile-data">Jul 28, 2010 4:56:06 PM org.biojava.bio.structure.io.PDBFileParser$JournalParser <init><br/></span><span class="compile-data">WARNING: 1TAP REF line not of correct length. Found 96, should be 48. Returning dummy JRNL object.<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.094 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructureToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.HeaderOnlyTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.228 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.PdbFileFormat30Test<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.ElementTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.SourceCompoundTest<br/></span><span class="compile-data">NumberformatException: For input string: "<http"<br/></span><span class="compile-data">NumberformatException: For input string: "/www."<br/></span><span class="compile-data">NumberformatException: For input string: "<http"<br/></span><span class="compile-data">NumberformatException: For input string: "/www."<br/></span><span class="compile-data">SOURCE INFO:<br/></span><span class="compile-data">Fragment? UNP RESIDUES 32-576<br/></span><span class="compile-data">Organism Scientific: MUS MUSCULUS<br/></span><span class="compile-data">Organism Tax Id: 10090<br/></span><span class="compile-data">Organism Common: MOUSE<br/></span><span class="compile-data">Gene: ACHE<br/></span><span class="compile-data">Expression System: HOMO SAPIENS<br/></span><span class="compile-data">Expression System Tax Id: 9606<br/></span><span class="compile-data">Expression System Strain: HEK293F<br/></span><span class="compile-data">Expression System Vector Type: PLASMID<br/></span><span class="compile-data">Expression System Plasmid: PCDNA3.1<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.437 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestDNAAlignment<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.scop.ScopTest<br/></span><span class="compile-data">parsed 110800 scop sunid domains.<br/></span><span class="compile-data">You did not specify PDBFileReader.setLoadChemCompInfo, need to fetch Chemical Components anyways.<br/></span><span class="compile-data">You did not specify PDBFileReader.setLoadChemCompInfo, need to fetch Chemical Components anyways.<br/></span><span class="compile-data">You did not specify PDBFileReader.setLoadChemCompInfo, need to fetch Chemical Components anyways.<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.269 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.341 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.FlipAFPChainTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.334 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.CeMainTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.FlipAFPChainTest<br/></span><span class="compile-data">mismatch in line: 170<br/></span><span class="compile-data">line1: <shift x="41.623" y="106.859" z="-13<br/></span><span class="compile-data">line2: <shift x="41.623" y="106.859" z="-14<br/></span><span class="compile-data">mismatch at position 40 c1: 3 4<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 36.865 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestSECalignment<br/></span><span class="compile-data">unknown char U<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.32 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.LoadOldXMLfileTest<br/></span><span class="compile-data">loading 1P80.D 2IUF.E<br/></span><span class="compile-data">AFPChainXMLParser: warning: pos1: 726 D:753 pos2: -1 E:1710 should never be -1. Probably parsing an.<br/></span><span class="compile-data">Ignore h1: 5 10 linePos: 5 >65:D <<br/></span><span class="compile-data">Ignore h1: 8 10 linePos: 8 >2:E <<br/></span><span class="compile-data">loading 1FEZ.A 1O08.A<br/></span><span class="compile-data">Ignore h1: 5 10 linePos: 5 >5:A <<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.416 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.Test1a4w<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.534 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.MMcifTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.974 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.TestAlignDBSearchPairs<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.484 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.PDBFileParserTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.Test4hhb<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.623 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.TestOutputStrings<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 49.525 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.ce.TestWebStartClient<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 44.121 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.ce.TestSmallAlignment<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestAtomCache<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 64, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">20 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/Group.java:289: warning - @return
tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:116: warning
- Tag @link: can't find setParseCAOnly in org.biojava.bio.structure.io.PDBFileReader<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:116: warning
- Tag @link: can't find setParseSecStruc in org.biojava.bio.structure.io.PDBFileReader<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:116: warning
- Tag @link: can't find setAlignSeqRes(boolean) in org.biojava.bio.structure.io.PDBFileReader<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/io/StructureIOFile.java:125:
warning - @param argument "params" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java:222:
warning - @param argument "string" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCat.java:59:
warning - @param argument "args" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainFlipper.java:43:
warning - @param argument "orig" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLConverter.java:22:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:72:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:57:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/xml/HasResultXMLConverter.java:56:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:159:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:159:
warning - Tag @link: can't find getStructure() in org.biojava.bio.structure.align.util.AtomCache<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:208:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/util/HTTPConnectionTools.java:247:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/util/HTTPConnectionTools.java:260:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1244:
warning - Tag @link: reference not found: CEMain#align()<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/model/AfpChainWriter.java:541:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure/src/main/java/org/biojava/bio/structure/align/model/AfpChainWriter.java:359:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 34 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/structure/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructureTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.731 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.benchmark.MultipleAlignmentTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.645 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructurePairAlignerTest<br/></span><span class="compile-data">Jul 28, 2010 4:59:50 PM org.biojava.bio.structure.io.PDBFileParser$JournalParser <init><br/></span><span class="compile-data">WARNING: 1TAP REF line not of correct length. Found 96, should be 48. Returning dummy JRNL object.<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.049 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructureToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.HeaderOnlyTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.169 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.PdbFileFormat30Test<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.ElementTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.SourceCompoundTest<br/></span><span class="compile-data">NumberformatException: For input string: "<http"<br/></span><span class="compile-data">NumberformatException: For input string: "/www."<br/></span><span class="compile-data">NumberformatException: For input string: "<http"<br/></span><span class="compile-data">NumberformatException: For input string: "/www."<br/></span><span class="compile-data">SOURCE INFO:<br/></span><span class="compile-data">Fragment? UNP RESIDUES 32-576<br/></span><span class="compile-data">Organism Scientific: MUS MUSCULUS<br/></span><span class="compile-data">Organism Tax Id: 10090<br/></span><span class="compile-data">Organism Common: MOUSE<br/></span><span class="compile-data">Gene: ACHE<br/></span><span class="compile-data">Expression System: HOMO SAPIENS<br/></span><span class="compile-data">Expression System Tax Id: 9606<br/></span><span class="compile-data">Expression System Strain: HEK293F<br/></span><span class="compile-data">Expression System Vector Type: PLASMID<br/></span><span class="compile-data">Expression System Plasmid: PCDNA3.1<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.422 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestDNAAlignment<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.scop.ScopTest<br/></span><span class="compile-data">parsed 110800 scop sunid domains.<br/></span><span class="compile-data">You did not specify PDBFileReader.setLoadChemCompInfo, need to fetch Chemical Components anyways.<br/></span><span class="compile-data">You did not specify PDBFileReader.setLoadChemCompInfo, need to fetch Chemical Components anyways.<br/></span><span class="compile-data">You did not specify PDBFileReader.setLoadChemCompInfo, need to fetch Chemical Components anyways.<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.241 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Not testing shift vectors for blocks > 1. There is still a problem...<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.383 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.FlipAFPChainTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.312 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.CeMainTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.FlipAFPChainTest<br/></span><span class="compile-data">mismatch in line: 170<br/></span><span class="compile-data">line1: <shift x="41.623" y="106.859" z="-13<br/></span><span class="compile-data">line2: <shift x="41.623" y="106.859" z="-14<br/></span><span class="compile-data">mismatch at position 40 c1: 3 4<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 36.771 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestSECalignment<br/></span><span class="compile-data">unknown char U<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.317 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.LoadOldXMLfileTest<br/></span><span class="compile-data">loading 1P80.D 2IUF.E<br/></span><span class="compile-data">AFPChainXMLParser: warning: pos1: 726 D:753 pos2: -1 E:1710 should never be -1. Probably parsing an.<br/></span><span class="compile-data">Ignore h1: 5 10 linePos: 5 >65:D <<br/></span><span class="compile-data">Ignore h1: 8 10 linePos: 8 >2:E <<br/></span><span class="compile-data">loading 1FEZ.A 1O08.A<br/></span><span class="compile-data">Ignore h1: 5 10 linePos: 5 >5:A <<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.Test1a4w<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.459 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.MMcifTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.764 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.TestAlignDBSearchPairs<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.425 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.PDBFileParserTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.Test4hhb<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.507 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.TestOutputStrings<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 49.221 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.ce.TestWebStartClient<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 44.36 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.ce.TestSmallAlignment<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestAtomCache<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 64, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure/target/biojava3-structure-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">489K uploaded (biojava3-structure-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-structure:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-structure'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-structure 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">421K uploaded (biojava3-structure-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure/3.0-SNAPSHOT/biojava3-structure-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">2078K uploaded (biojava3-structure-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building das<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/das/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/das/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 91 source files to /opt/cruise/projects/biojava-svn/das/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 5 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 9 source files to /opt/cruise/projects/biojava-svn/das/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/das/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.dasobert.TestRegistry<br/></span><span class="compile-data">Das2SourceHandler: source size: 811<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.495 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestInteractionParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestExternalSource<br/></span><span class="compile-data">Das2SourceHandler: source size: 46<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.562 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSisyphusServer<br/></span><span class="compile-data">Jul 28, 2010 5:04:18 PM org.biojava.dasobert.das.AlignmentThread retrieveAlignments<br/></span><span class="compile-data">INFO: requesting alignment http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468<br/></span><span class="compile-data">object: CONSTRUCT:35<br/></span><span class="compile-data">object: CONSTRUCT:36<br/></span><span class="compile-data">object: CONSTRUCT:37<br/></span><span class="compile-data">object: CONSTRUCT:38<br/></span><span class="compile-data">object: CONSTRUCT:39<br/></span><span class="compile-data">object: CONSTRUCT:40<br/></span><span class="compile-data">object: CONSTRUCT:41<br/></span><span class="compile-data">object: CONSTRUCT:42<br/></span><span class="compile-data">object: CONSTRUCT:43<br/></span><span class="compile-data">object: CONSTRUCT:44<br/></span><span class="compile-data">object: CONSTRUCT:45<br/></span><span class="compile-data">object: CONSTRUCT:46<br/></span><span class="compile-data">object: CONSTRUCT:47<br/></span><span class="compile-data">object: CONSTRUCT:48<br/></span><span class="compile-data">object: CONSTRUCT:49<br/></span><span class="compile-data">object: CONSTRUCT:50<br/></span><span class="compile-data">object: CONSTRUCT:51<br/></span><span class="compile-data">object: CONSTRUCT:52<br/></span><span class="compile-data">object: CONSTRUCT:53<br/></span><span class="compile-data">object: CONSTRUCT:54<br/></span><span class="compile-data">object: CONSTRUCT:55<br/></span><span class="compile-data">number of blocks: 4<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.904 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSequenceParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSourcesParse<br/></span><span class="compile-data">unsupported capability: das1:dna<br/></span><span class="compile-data">Das2SourceHandler: source size: 267<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestUCSCFeatures<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.server.TestServers<br/></span><span class="compile-data">Jul 28, 2010 5:04:19 PM org.biojava.dasobert.das.SequenceThread retrieveSequence<br/></span><span class="compile-data">INFO: requesting sequence from http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=P50225<br/></span><span class="compile-data">MELIQDTSRPPLEYVKGVPLIKYFAEALGPLQSFQARPDDLLISTYPKSGTTWVSQILDMIYQGGDLEKCHRAPIFMRVPFLEFKAPGIPSGMETLKDTPAPRLLKTHLPLALLPQTLLDQKVKVVYVARNAKDVAVSYYHFYHMAKVHPEPGTWDSFLEKFMVGEVSYGSWYQHVQEWWELSRTHPVLYLFYEDMKENPKREIQKILEFVGRSLPEETVDFMVQHTSFKEMKKNPMTNYTTVPQEFMDHSISPFMRKGMAGDWKTTFTVAQNERFDADYAEKMAGCSLSFRSEL<br/></span><span class="compile-data">started getInteractions method<br/></span><span class="compile-data">java.io.IOException: Server returned HTTP response code: 500 for URL: http://dasmi.bioinf.mpi-inf.mpg.de/das/intact/interaction?interactor=1212<br/></span><span class="compile-data"> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)<br/></span><span class="compile-data"> at java.lang.reflect.Constructor.newInstance(Constructor.java:532)<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1324)<br/></span><span class="compile-data"> at java.security.AccessController.doPrivileged(Native Method)<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1318)<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:972)<br/></span><span class="compile-data"> at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:188)<br/></span><span class="compile-data"> at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:136)<br/></span><span class="compile-data"> at org.biojava.dasobert.das.InteractionThread.retrieveInteractions(InteractionThread.java:163)<br/></span><span class="compile-data"> at org.biojava.dasobert.das.InteractionThread.getInteractions(InteractionThread.java:134)<br/></span><span class="compile-data"> at org.biojava.dasobert.server.TestServers.testInteractionServer(TestServers.java:86)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Caused by: java.io.IOException: Server returned HTTP response code: 500 for URL: http://dasmi.bioinf.mpi-inf.mpg.de/das/intact/interaction?interactor=1212<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1269)<br/></span><span class="compile-data"> at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:391)<br/></span><span class="compile-data"> at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:163)<br/></span><span class="compile-data"> ... 27 more<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.89 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestFeatureParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">6 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Detail.java:143: warning - @return
tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:178: warning -
@param argument "interactors" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:187: warning -
@param argument "ref" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interactor.java:237: warning -
@returntrue is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/das/src/main/java/org/biojava/dasobert/das/Capabilities.java:58: warning - @return
tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/das/src/main/java/org/biojava/dasobert/das2/io/DASRegistryCoordinatesReaderXML.java:56:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/das/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 5 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/das/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.dasobert.TestRegistry<br/></span><span class="compile-data">Das2SourceHandler: source size: 811<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.098 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestInteractionParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestExternalSource<br/></span><span class="compile-data">Das2SourceHandler: source size: 46<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.877 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSisyphusServer<br/></span><span class="compile-data">Jul 28, 2010 5:04:39 PM org.biojava.dasobert.das.AlignmentThread retrieveAlignments<br/></span><span class="compile-data">INFO: requesting alignment http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468<br/></span><span class="compile-data">object: CONSTRUCT:35<br/></span><span class="compile-data">object: CONSTRUCT:36<br/></span><span class="compile-data">object: CONSTRUCT:37<br/></span><span class="compile-data">object: CONSTRUCT:38<br/></span><span class="compile-data">object: CONSTRUCT:39<br/></span><span class="compile-data">object: CONSTRUCT:40<br/></span><span class="compile-data">object: CONSTRUCT:41<br/></span><span class="compile-data">object: CONSTRUCT:42<br/></span><span class="compile-data">object: CONSTRUCT:43<br/></span><span class="compile-data">object: CONSTRUCT:44<br/></span><span class="compile-data">object: CONSTRUCT:45<br/></span><span class="compile-data">object: CONSTRUCT:46<br/></span><span class="compile-data">object: CONSTRUCT:47<br/></span><span class="compile-data">object: CONSTRUCT:48<br/></span><span class="compile-data">object: CONSTRUCT:49<br/></span><span class="compile-data">object: CONSTRUCT:50<br/></span><span class="compile-data">object: CONSTRUCT:51<br/></span><span class="compile-data">object: CONSTRUCT:52<br/></span><span class="compile-data">object: CONSTRUCT:53<br/></span><span class="compile-data">object: CONSTRUCT:54<br/></span><span class="compile-data">object: CONSTRUCT:55<br/></span><span class="compile-data">number of blocks: 4<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.792 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSequenceParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSourcesParse<br/></span><span class="compile-data">unsupported capability: das1:dna<br/></span><span class="compile-data">Das2SourceHandler: source size: 267<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestUCSCFeatures<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.server.TestServers<br/></span><span class="compile-data">Jul 28, 2010 5:04:40 PM org.biojava.dasobert.das.SequenceThread retrieveSequence<br/></span><span class="compile-data">INFO: requesting sequence from http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=P50225<br/></span><span class="compile-data">MELIQDTSRPPLEYVKGVPLIKYFAEALGPLQSFQARPDDLLISTYPKSGTTWVSQILDMIYQGGDLEKCHRAPIFMRVPFLEFKAPGIPSGMETLKDTPAPRLLKTHLPLALLPQTLLDQKVKVVYVARNAKDVAVSYYHFYHMAKVHPEPGTWDSFLEKFMVGEVSYGSWYQHVQEWWELSRTHPVLYLFYEDMKENPKREIQKILEFVGRSLPEETVDFMVQHTSFKEMKKNPMTNYTTVPQEFMDHSISPFMRKGMAGDWKTTFTVAQNERFDADYAEKMAGCSLSFRSEL<br/></span><span class="compile-data">started getInteractions method<br/></span><span class="compile-data">java.io.IOException: Server returned HTTP response code: 500 for URL: http://dasmi.bioinf.mpi-inf.mpg.de/das/intact/interaction?interactor=1212<br/></span><span class="compile-data"> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)<br/></span><span class="compile-data"> at java.lang.reflect.Constructor.newInstance(Constructor.java:532)<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1324)<br/></span><span class="compile-data"> at java.security.AccessController.doPrivileged(Native Method)<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1318)<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:972)<br/></span><span class="compile-data"> at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:188)<br/></span><span class="compile-data"> at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:136)<br/></span><span class="compile-data"> at org.biojava.dasobert.das.InteractionThread.retrieveInteractions(InteractionThread.java:163)<br/></span><span class="compile-data"> at org.biojava.dasobert.das.InteractionThread.getInteractions(InteractionThread.java:134)<br/></span><span class="compile-data"> at org.biojava.dasobert.server.TestServers.testInteractionServer(TestServers.java:86)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Caused by: java.io.IOException: Server returned HTTP response code: 500 for URL: http://dasmi.bioinf.mpi-inf.mpg.de/das/intact/interaction?interactor=1212<br/></span><span class="compile-data"> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1269)<br/></span><span class="compile-data"> at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:391)<br/></span><span class="compile-data"> at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:163)<br/></span><span class="compile-data"> ... 27 more<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.714 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestFeatureParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/das/target/das-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">175K uploaded (das-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:das:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:das'<br/></span><span class="compile-data">[INFO] Uploading project information for das 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">142K uploaded (das-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/3.0-SNAPSHOT/das-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">809K uploaded (das-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequence<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>site:attach-descriptor {execution: default-attach-descriptor}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/pom.xml to /home/andreas/.m2/repository/org/biojava/sequence/3.0-SNAPSHOT/sequence-3.0-SNAPSHOT.pom<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Not executing Javadoc as the project is not a Java classpath-capable package<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>site:attach-descriptor {execution: default-attach-descriptor}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/pom.xml to /home/andreas/.m2/repository/org/biojava/sequence/3.0-SNAPSHOT/sequence-3.0-SNAPSHOT.pom<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence/3.0-SNAPSHOT/sequence-3.0-SNAPSHOT.pom<br/></span><span class="compile-data">768b uploaded (sequence-3.0-SNAPSHOT.pom)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequence'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequence:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequence-core<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/sequence/sequence-core/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 32 source files to /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 3 source files to /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">There are no tests to run.<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">5 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:108:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:83:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:96:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:71:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:81:
warning - @param argument "species" is not a parameter name.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-core/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">There are no tests to run.<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT-sources.jar to
/home/andreas/.m2/repository/org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-core/target/sequence-core-3.0-SNAPSHOT-javadoc.jar to
/home/andreas/.m2/repository/org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">40K uploaded (sequence-core-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequence-core'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequence-core:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for sequence-core 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">30K uploaded (sequence-core-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-core/3.0-SNAPSHOT/sequence-core-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">295K uploaded (sequence-core-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequence-rna<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/sequence/sequence-rna/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-rna/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-rna/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] JAR will be empty - no content was marked for inclusion!<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-rna/target/sequence-rna-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-rna/target/sequence-rna-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-rna/3.0-SNAPSHOT/sequence-rna-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-rna/target/sequence-rna-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-rna/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-rna/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] JAR will be empty - no content was marked for inclusion!<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-rna/target/sequence-rna-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-rna/3.0-SNAPSHOT/sequence-rna-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-rna/target/sequence-rna-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/sequence-rna/3.0-SNAPSHOT/sequence-rna-3.0-SNAPSHOT-sources.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-rna/3.0-SNAPSHOT/sequence-rna-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">1K uploaded (sequence-rna-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Uploading project information for sequence-rna 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequence-rna:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequence-rna'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-rna/3.0-SNAPSHOT/sequence-rna-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">738b uploaded (sequence-rna-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequence-biosql<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 41 source files to /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-biosql/target/sequence-biosql-3.0-SNAPSHOT-javadoc.jar
to /home/andreas/.m2/repository/org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">66K uploaded (sequence-biosql-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequence-biosql'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequence-biosql:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for sequence-biosql 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">57K uploaded (sequence-biosql-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-biosql/3.0-SNAPSHOT/sequence-biosql-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">336K uploaded (sequence-biosql-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequence-fasta<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] JAR will be empty - no content was marked for inclusion!<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/target/sequence-fasta-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/target/sequence-fasta-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-fasta/3.0-SNAPSHOT/sequence-fasta-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/target/sequence-fasta-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] JAR will be empty - no content was marked for inclusion!<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/target/sequence-fasta-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequence-fasta/3.0-SNAPSHOT/sequence-fasta-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-fasta/target/sequence-fasta-3.0-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/sequence-fasta/3.0-SNAPSHOT/sequence-fasta-3.0-SNAPSHOT-sources.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-fasta/3.0-SNAPSHOT/sequence-fasta-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">1K uploaded (sequence-fasta-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequence-fasta'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequence-fasta:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for sequence-fasta 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-fasta/3.0-SNAPSHOT/sequence-fasta-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">746b uploaded (sequence-fasta-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequence-blastxml<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jaxb2:generate {execution: default}</td>
</tr>
<tr>
<td><span class="compile-data">Cannot find CatalogManager.properties<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 13 source files to /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No sources to compile<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT.jar to
/home/andreas/.m2/repository/org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jaxb2:generate {execution: default}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Skipped XJC execution. Generated sources were up-to-date.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jaxb2:generate {execution: default}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Skipped XJC execution. Generated sources were up-to-date.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No sources to compile<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT.jar to
/home/andreas/.m2/repository/org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequence/sequence-blastxml/target/sequence-blastxml-3.0-SNAPSHOT-javadoc.jar
to /home/andreas/.m2/repository/org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">16K uploaded (sequence-blastxml-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequence-blastxml'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequence-blastxml:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for sequence-blastxml 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">16K uploaded (sequence-blastxml-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequence-blastxml/3.0-SNAPSHOT/sequence-blastxml-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">120K uploaded (sequence-blastxml-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequencing<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/sequencing/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequencing/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 28 source files to /opt/cruise/projects/biojava-svn/sequencing/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 74 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 11 source files to /opt/cruise/projects/biojava-svn/sequencing/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/sequencing/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqBuilderTest<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqReaderTest<br/></span><span class="compile-data">Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqVariantTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 129, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/sequencing/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/sequencing/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 74 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/sequencing/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqBuilderTest<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqReaderTest<br/></span><span class="compile-data">Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqVariantTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 129, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/sequencing/target/sequencing-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">76K uploaded (sequencing-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequencing'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequencing:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for sequencing 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">63K uploaded (sequencing-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/3.0-SNAPSHOT/sequencing-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">372K uploaded (sequencing-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building phylo<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/phylo/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/phylo/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 37 source files to /opt/cruise/projects/biojava-svn/phylo/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/phylo/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/phylo/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.191 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">1 warning<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/TreesBlock.java:640: warning
- Tag @link: can't find getTreeAsJGraphT(java.lang.String) in org.biojavax.bio.phylo.io.nexus.TreesBlock<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/phylo/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/phylo/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.191 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/phylo/target/phylo-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">78K uploaded (phylo-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:phylo:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for phylo 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:phylo'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">60K uploaded (phylo-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/3.0-SNAPSHOT/phylo-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">404K uploaded (phylo-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biosql<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biosql/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biosql/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 35 source files to /opt/cruise/projects/biojava-svn/biosql/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biosql/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 2 source files to /opt/cruise/projects/biojava-svn/biosql/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biosql/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest<br/></span><span class="compile-data">No hsqldb driver found.<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biosql/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biosql/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biosql/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest<br/></span><span class="compile-data">No hsqldb driver found.<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biosql/target/biosql-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">164K uploaded (biosql-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biosql'<br/></span><span class="compile-data">[INFO] Uploading project information for biosql 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biosql:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">135K uploaded (biosql-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/3.0-SNAPSHOT/biosql-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">670K uploaded (biosql-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building gui<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/gui/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/gui/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 99 source files to /opt/cruise/projects/biojava-svn/gui/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/gui/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/gui/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/gui/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/gui/target/gui-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">232K uploaded (gui-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:gui'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:gui:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for gui 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">170K uploaded (gui-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/3.0-SNAPSHOT/gui-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">1110K uploaded (gui-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-core<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-core/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 108 source files to /opt/cruise/projects/biojava-svn/biojava3-core/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 4 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 12 source files to /opt/cruise/projects/biojava-svn/biojava3-core/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.core.sequence.location.LocationParserTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.JoiningSequenceReaderTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.EditSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.io.FastaReaderTest<br/></span><span class="compile-data">process<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.io.GenericFastaHeaderParserTest<br/></span><span class="compile-data">parseHeader<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.TranslationTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.733 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.io.FastaWriterTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.location.LocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 23, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">55 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:153:
warning - Tag @link: can't find countCompounds(org.biojava3.core.sequence.template.Sequence, C[]) in org.biojava3.core.sequence.template.SequenceMixin<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:161:
warning - Tag @link: reference not found: SequenceMixin.SequenceIterator<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:161:
warning - Tag @link: reference not found: SequenceMixin.SequenceIterator<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:63: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java:178: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java:142: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java:204: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java:159: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java:124: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java:55: warning
- @param argument "parentDNASequence" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:94:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:119:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:71:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:204:
warning - @param argument "startCodonSequence" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:219:
warning - @param argument "stopCodonSequence" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java:57:
warning - Tag @link: can't find getAllSubLocations() in org.biojava3.core.sequence.location.template.Location<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java:155:
warning - @param argument "location" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/BufferedReaderBytesRead.java:105:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:70:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:41:
warning - @param argument "br" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:37:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:53:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaWriterHelper.java:80:
warning - @param argument "dnaSequences" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/util/IOUtils.java:168:
warning - Tag @link: can't find processReader(String) in org.biojava3.core.sequence.io.util.IOUtils<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:366:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:357:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:124:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:97:
warning - @param argument "bioBegin" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:115:
warning - @param argument "bioEnd" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:147:
warning - @param argument "annotation" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:315:
warning - @param argument "species" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:214:
warning - Tag @link: reference not found: SequenceBackingStore<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:135:
warning - Tag @link: can't find toString() in org.biojava3.core.sequence.template.Compound<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:214:
warning - Tag @link: reference not found: SequenceBackingStore<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Table.java:17:
warning - Tag @link: reference not found: IUPACTable<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:41:
warning - @ is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:41:
warning - @link{AminoAcidCompound is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:41:
warning - @ is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:41:
warning - @link{AminoAcidCompound is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:133:
warning - Tag @link: reference not found: TranslationEngine<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:53:
warning - @ is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:53:
warning - @ is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:133:
warning - Tag @link: reference not found: TranslationEngine<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Table.java:17:
warning - Tag @link: reference not found: IUPACTable<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:133:
warning - Tag @link: reference not found: TranslationEngine<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:214:
warning - Tag @link: reference not found: SequenceBackingStore<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:214:
warning - Tag @link: reference not found: SequenceBackingStore<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:214:
warning - Tag @link: reference not found: SequenceBackingStore<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Table.java:17:
warning - Tag @link: reference not found: IUPACTable<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Table.java:17:
warning - Tag @link: reference not found: IUPACTable<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:133:
warning - Tag @link: reference not found: TranslationEngine<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:161:
warning - Tag @link: reference not found: SequenceMixin.SequenceIterator<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java:214:
warning - Tag @link: reference not found: SequenceBackingStore<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Table.java:17:
warning - Tag @link: reference not found: IUPACTable<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:133:
warning - Tag @link: reference not found: TranslationEngine<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 4 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.core.sequence.location.LocationParserTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.JoiningSequenceReaderTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.EditSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.io.FastaReaderTest<br/></span><span class="compile-data">process<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.io.GenericFastaHeaderParserTest<br/></span><span class="compile-data">parseHeader<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.TranslationTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.733 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.io.FastaWriterTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.location.LocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 23, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">203K uploaded (biojava3-core-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-core 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-core:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-core'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">131K uploaded (biojava3-core-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-core/3.0-SNAPSHOT/biojava3-core-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">1169K uploaded (biojava3-core-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-phylo<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-phylo/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 10 source files to /opt/cruise/projects/biojava-svn/biojava3-phylo/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-phylo/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/biojava3-phylo/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.phylo.AppTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">2 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-phylo/src/main/java/org/biojava3/phylo/Comparison.java:24: warning - @param
argument "s1" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-phylo/src/main/java/org/biojava3/phylo/Comparison.java:24: warning - @param
argument "s2" is not a parameter name.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-phylo/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.phylo.AppTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">57K uploaded (biojava3-phylo-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-phylo:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-phylo 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-phylo'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">50K uploaded (biojava3-phylo-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-phylo/3.0-SNAPSHOT/biojava3-phylo-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">99K uploaded (biojava3-phylo-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-structure-gui<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/structure-gui/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 14 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 82 source files to /opt/cruise/projects/biojava-svn/structure-gui/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/structure-gui/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 6 source files to /opt/cruise/projects/biojava-svn/structure-gui/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/structure-gui/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.structure.gui.StructureViewerTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec<br/></span><span class="compile-data">Running org.biojava.structure.gui.ViewerTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.structure.gui.RenderStyleTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.gui.TestAtomInfo<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.structure.gui.JmolViewerImplTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">21 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/gui/SequenceDisplay.java:213:
warning: unmappable character for encoding UTF-8<br/></span><span class="compile-data">[WARNING] //residueSizeSl?ider.setMinorTickSpacing(2);<br/></span><span class="compile-data">[WARNING] ^<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java:483:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java:183:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MenuCreator.java:257:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/StructureAlignmentDisplay.java:30:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/StructureAlignmentDisplay.java:73:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/SystemInfo.java:147:
warning - @usage is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolTools.java:22:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/RasmolCommandListener.java:46:
warning - Tag @link: reference not found: BiojavaJmol<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:137:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:171:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:106:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:73:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:65:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:82:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:82:
warning - @param argument "x" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:106:
warning - @param argument "aligSeq," is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java:171:
warning - @param argument "rowNr" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava3/structure/gui/StructureViewer.java:26:
warning - @param argument "RenderStyle" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/RasmolCommandListener.java:46:
warning - Tag @link: reference not found: BiojavaJmol<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/RasmolCommandListener.java:46:
warning - Tag @link: reference not found: BiojavaJmol<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 14 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/structure-gui/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/structure-gui/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/structure-gui/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/structure-gui/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.structure.gui.StructureViewerTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec<br/></span><span class="compile-data">Running org.biojava.structure.gui.ViewerTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.structure.gui.RenderStyleTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.gui.TestAtomInfo<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.structure.gui.JmolViewerImplTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT-sources.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/structure-gui/target/biojava3-structure-gui-3.0-SNAPSHOT-javadoc.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">237K uploaded (biojava3-structure-gui-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-structure-gui'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-structure-gui:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-structure-gui 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">154K uploaded (biojava3-structure-gui-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure-gui/3.0-SNAPSHOT/biojava3-structure-gui-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">823K uploaded (biojava3-structure-gui-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-alignment<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-alignment/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 19 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 46 source files to /opt/cruise/projects/biojava-svn/biojava3-alignment/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 2 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 18 source files to /opt/cruise/projects/biojava-svn/biojava3-alignment/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.alignment.FractionalSimilarityScorerTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleSubstitutionMatrixTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.056 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfilePairTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.GuideTreeTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileTest<br/></span><span class="compile-data">Tests run: 53, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.075 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SmithWatermanTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleSequencePairTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleGapPenaltyTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileProfileAlignerTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleAlignedSequenceTest<br/></span><span class="compile-data">Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.035 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.NeedlemanWunschTest<br/></span><span class="compile-data">Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.FractionalIdentityScorerTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 205, Failures: 0, Errors: 0, Skipped: 4<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">6 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-alignment/src/main/java/org/biojava3/alignment/Alignments.java:129: warning
- @param argument "type" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-alignment/src/main/java/org/biojava3/alignment/template/GuideTreeNode.java:98:
warning - @param argument "profile" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java:46:
warning - Tag @link: reference not found: AlignedSequences<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java:46:
warning - Tag @link: reference not found: AlignedSequences<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java:46:
warning - Tag @link: reference not found: AlignedSequences<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java:46:
warning - Tag @link: reference not found: AlignedSequences<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 19 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 2 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.alignment.FractionalSimilarityScorerTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleSubstitutionMatrixTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfilePairTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.GuideTreeTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileTest<br/></span><span class="compile-data">Tests run: 53, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.075 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SmithWatermanTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleSequencePairTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleGapPenaltyTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileProfileAlignerTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleAlignedSequenceTest<br/></span><span class="compile-data">Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.NeedlemanWunschTest<br/></span><span class="compile-data">Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.FractionalIdentityScorerTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 205, Failures: 0, Errors: 0, Skipped: 4<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT-sources.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-SNAPSHOT-javadoc.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">89K uploaded (biojava3-alignment-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-alignment'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-alignment 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-alignment:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">79K uploaded (biojava3-alignment-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-alignment/3.0-SNAPSHOT/biojava3-alignment-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">520K uploaded (biojava3-alignment-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-genome<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-genome/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 19 source files to /opt/cruise/projects/biojava-svn/biojava3-genome/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/biojava3-genome/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-genome/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.genome.AppTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">3 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:66: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java:33:
warning - @param argument "fileName" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java:33:
warning - @param argument "chromosomeSequence" is not a parameter name.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-genome/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.genome.AppTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">55K uploaded (biojava3-genome-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-genome'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-genome 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-genome:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">38K uploaded (biojava3-genome-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-genome/3.0-SNAPSHOT/biojava3-genome-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">232K uploaded (biojava3-genome-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-protmod<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-protmod/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 14 source files to /opt/cruise/projects/biojava-svn/biojava3-protmod/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 3 source files to /opt/cruise/projects/biojava-svn/biojava3-protmod/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.protmod.parser.ProteinModificationParserTest<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3HN3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CPO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AL2<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1L9H<br/></span><span class="compile-data">1L9H 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">1L9H 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BDO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AT9<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ALL<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1B8D<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1OGP<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EL5<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1W1O<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DII<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2KJS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D7E<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2TMD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1VAO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1PDA<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2J96<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2HIL<br/></span><span class="compile-data">2HIL 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 E: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 F: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 G: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 H: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 J: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 K: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 L: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 M: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 N: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 O: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 P: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 Q: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 R: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FEH<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1N63<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1HXQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1QI9<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1XG0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2HIL<br/></span><span class="compile-data">2HIL 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 E: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 F: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 G: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 H: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 J: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 K: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 L: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 M: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 N: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 O: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 P: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 Q: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 R: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3I3L<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3MVJ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3MVJ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1KZU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AA6<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1NT0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ERM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1QGW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2G66<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2G66<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A39<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AG7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D5W<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1H9C<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EUD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1NSQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3LXN<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ZM2<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E0Z<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DM3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2NPP<br/></span><span class="compile-data">2NPP 0 X: Overlapping between ligands and residues<br/></span><span class="compile-data">2NPP 0 Y: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1GK8<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DOJ<br/></span><span class="compile-data">1DOJ 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DOJ<br/></span><span class="compile-data">1DOJ 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1G42<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2B2U<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2B2U<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ALL<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3FMY<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1IV8<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1IV8<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ZTO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D7T<br/></span><span class="compile-data">1D7T 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D5M<br/></span><span class="compile-data">1D5M 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2H9E<br/></span><span class="compile-data">2H9E 0 S: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1YYL<br/></span><span class="compile-data">1YYL 0 M: Overlapping between ligands and residues<br/></span><span class="compile-data">1YYL 0 S: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AEX<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1OMW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2C0J<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AA1<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1O5K<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A8I<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2J4Y<br/></span><span class="compile-data">2J4Y 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">2J4Y 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A2V<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JJU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1WCT<br/></span><span class="compile-data">1WCT 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A2C<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1WCT<br/></span><span class="compile-data">1WCT 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AUK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">148L<br/></span><span class="compile-data">Hetatom null DAL false 3 does not align with Hetatom 165 AMU true atoms: 18 5<br/></span><span class="compile-data">they seem to be hetatoms, so ignoring mismatch.<br/></span><span class="compile-data">148L 0 S: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1C4B<br/></span><span class="compile-data">1C4B 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1T5M<br/></span><span class="compile-data">1T5M 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CZQ<br/></span><span class="compile-data">1CZQ 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">1CZQ 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2JUE<br/></span><span class="compile-data">2JUE 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A7Y<br/></span><span class="compile-data">1A7Y 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">1A7Y 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">1A7Y 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CXP<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1F8W<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FFV<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CKN<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BUW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CZI<br/></span><span class="compile-data">1CZI 0 P: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E93<br/></span><span class="compile-data">Jul 28, 2010 5:21:57 PM org.biojava.bio.structure.io.PDBFileParser$JournalParser <init><br/></span><span class="compile-data">WARNING: 1E93 REF line not of correct length. Found 55, should be 48. Returning dummy JRNL object.<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ACD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1C0T<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BI0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1HBM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FFU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3H5R<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JQ7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1J6Z<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1B80<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CWM<br/></span><span class="compile-data">1CWM 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BCK<br/></span><span class="compile-data">1BCK 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EA7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1TYS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EBV<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2VZK<br/></span><span class="compile-data">2VZK 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">2VZK 0 F: Overlapping between ligands and residues<br/></span><span class="compile-data">2VZK 0 H: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IU4<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1Y9A<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IUW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1K83<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2VH3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2AOC<br/></span><span class="compile-data">2AOC 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DSR<br/></span><span class="compile-data">1DSR 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AIQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CF0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CTP<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3L4M<br/></span><span class="compile-data">===<br/></span><span class="compile-data">4ECA<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3M6S<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A6L<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A70<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1RPB<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3B2M<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CAD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FP4<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1M1N<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1G7K<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EMA<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2JE3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FWX<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1QNI<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IWF<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IWK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1SU6<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1SU7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JJU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JJU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1PXQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1PXQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ITK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1R30<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1NGK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1YZW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1XQM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1UIS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2OJK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2A46<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1YZW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1XQM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1UIS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2OJK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2A46<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2AXR<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2QH7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3EE4<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3H8L<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 582.26 sec<br/></span><span class="compile-data">Running org.biojava3.protmod.ProteinModificationRegistryTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">11 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/Component.java:43: warning
- Tag @link: reference not found: register<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/Component.java:43: warning
- Tag @link: reference not found: of<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63:
warning - @param argument "labelOfAtomOnComponent1" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63:
warning - @param argument "labelOfAtomOnComponent2" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86:
warning - @param argument "labelOfAtomOnComponent1" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86:
warning - @param argument "labelOfAtomOnComponent2" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModifiedCompoundImpl.java:57:
warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation:
method.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModifiedCompoundImpl.java:74:
warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation:
method.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ModifiedCompoundImpl.java:91:
warning - @param argument "otherGroups" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/ProteinModification.java:55:
warning - Tag @link: reference not found: register<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/parser/DefaultProteinModificationParser.java:85:
warning - @param argument "recordUnidentifiableAtomLinkages" is not a parameter name.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava3.protmod.parser.ProteinModificationParserTest<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3HN3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CPO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AL2<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1L9H<br/></span><span class="compile-data">1L9H 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">1L9H 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BDO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AT9<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ALL<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1B8D<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1OGP<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EL5<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1W1O<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DII<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2KJS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D7E<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2TMD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1VAO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1PDA<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2J96<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2HIL<br/></span><span class="compile-data">2HIL 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 E: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 F: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 G: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 H: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 J: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 K: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 L: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 M: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 N: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 O: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 P: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 Q: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 R: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FEH<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1N63<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1HXQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1QI9<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1XG0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2HIL<br/></span><span class="compile-data">2HIL 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 E: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 F: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 G: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 H: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 J: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 K: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 L: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 M: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 N: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 O: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 P: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 Q: Overlapping between ligands and residues<br/></span><span class="compile-data">2HIL 0 R: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3I3L<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3MVJ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3MVJ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1KZU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AA6<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1NT0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ERM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1QGW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2G66<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2G66<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">AminoAcid SEQRES:PRO P null false SEQRES 10 does not align with AminoAcid ATOM:HY3 P 13 true ATOM atoms: 8 10<br/></span><span class="compile-data">org.biojava.bio.structure.StructureException: could not match residues<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.mapChains(SeqRes2AtomAligner.java:347)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:277)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:153)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2271)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2170)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2024)<br/></span><span class="compile-data"> at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:488)<br/></span><span class="compile-data"> at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:283)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.parserTest(ProteinModificationParserTest.java:253)<br/></span><span class="compile-data"> at org.biojava3.protmod.parser.ProteinModificationParserTest.testMultiParser(ProteinModificationParserTest.java:243)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:154)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:127)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:106)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:124)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:109)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:118)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:208)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:203)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A39<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AG7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D5W<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1H9C<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EUD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1NSQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3LXN<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ZM2<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E0Z<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DM3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2NPP<br/></span><span class="compile-data">2NPP 0 X: Overlapping between ligands and residues<br/></span><span class="compile-data">2NPP 0 Y: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1GK8<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DOJ<br/></span><span class="compile-data">1DOJ 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DOJ<br/></span><span class="compile-data">1DOJ 0 I: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1G42<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2B2U<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2B2U<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ALL<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3FMY<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1IV8<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1IV8<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ZTO<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D7T<br/></span><span class="compile-data">1D7T 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1D5M<br/></span><span class="compile-data">1D5M 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2H9E<br/></span><span class="compile-data">2H9E 0 S: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1YYL<br/></span><span class="compile-data">1YYL 0 M: Overlapping between ligands and residues<br/></span><span class="compile-data">1YYL 0 S: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AEX<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1OMW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2C0J<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AA1<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1O5K<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A8I<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2J4Y<br/></span><span class="compile-data">2J4Y 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">2J4Y 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A2V<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JJU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1WCT<br/></span><span class="compile-data">1WCT 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A2C<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1WCT<br/></span><span class="compile-data">1WCT 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AUK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">148L<br/></span><span class="compile-data">Hetatom null DAL false 3 does not align with Hetatom 165 AMU true atoms: 18 5<br/></span><span class="compile-data">they seem to be hetatoms, so ignoring mismatch.<br/></span><span class="compile-data">148L 0 S: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1C4B<br/></span><span class="compile-data">1C4B 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1T5M<br/></span><span class="compile-data">1T5M 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CZQ<br/></span><span class="compile-data">1CZQ 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">1CZQ 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2JUE<br/></span><span class="compile-data">2JUE 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A7Y<br/></span><span class="compile-data">1A7Y 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">1A7Y 0 B: Overlapping between ligands and residues<br/></span><span class="compile-data">1A7Y 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CXP<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1F8W<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FFV<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CKN<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BUW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CZI<br/></span><span class="compile-data">1CZI 0 P: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E93<br/></span><span class="compile-data">Jul 28, 2010 5:31:50 PM org.biojava.bio.structure.io.PDBFileParser$JournalParser <init><br/></span><span class="compile-data">WARNING: 1E93 REF line not of correct length. Found 55, should be 48. Returning dummy JRNL object.<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ACD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1C0T<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BI0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1E6Y<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1HBM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FFU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3H5R<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JQ7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1J6Z<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1B80<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CWM<br/></span><span class="compile-data">1CWM 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1BCK<br/></span><span class="compile-data">1BCK 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EA7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1TYS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EBV<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2VZK<br/></span><span class="compile-data">2VZK 0 D: Overlapping between ligands and residues<br/></span><span class="compile-data">2VZK 0 F: Overlapping between ligands and residues<br/></span><span class="compile-data">2VZK 0 H: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IU4<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1Y9A<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IUW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1K83<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2VH3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2AOC<br/></span><span class="compile-data">2AOC 0 C: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1DSR<br/></span><span class="compile-data">1DSR 0 A: Overlapping between ligands and residues<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1AIQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CF0<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CTP<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3L4M<br/></span><span class="compile-data">===<br/></span><span class="compile-data">4ECA<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3M6S<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A6L<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1A70<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1RPB<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3B2M<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1CAD<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FP4<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1M1N<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1G7K<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1EMA<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2JE3<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1FWX<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1QNI<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IWF<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2IWK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1SU6<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1SU7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JJU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1JJU<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1PXQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1PXQ<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1ITK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1R30<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1NGK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1YZW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1XQM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1UIS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2OJK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2A46<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1YZW<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1XQM<br/></span><span class="compile-data">===<br/></span><span class="compile-data">1UIS<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2OJK<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2A46<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2AXR<br/></span><span class="compile-data">===<br/></span><span class="compile-data">2QH7<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3EE4<br/></span><span class="compile-data">===<br/></span><span class="compile-data">3H8L<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 584.322 sec<br/></span><span class="compile-data">Running org.biojava3.protmod.ProteinModificationRegistryTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">59K uploaded (biojava3-protmod-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-protmod:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-protmod'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-protmod 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">48K uploaded (biojava3-protmod-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-protmod/3.0-SNAPSHOT/biojava3-protmod-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">166K uploaded (biojava3-protmod-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-ws<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-ws/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 3 source files to /opt/cruise/projects/biojava-svn/biojava3-ws/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-ws/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">There are no tests to run.<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 0 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-ws/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">There are no tests to run.<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT.jar<br/></span><span class="compile-data">3K uploaded (biojava3-ws-3.0-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-ws'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-ws 3.0-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-ws:3.0-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT-sources.jar<br/></span><span class="compile-data">4K uploaded (biojava3-ws-3.0-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-ws/3.0-SNAPSHOT/biojava3-ws-3.0-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">40K uploaded (biojava3-ws-3.0-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] <br/></span><span class="compile-data">[INFO] <br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Reactor Summary:<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] biojava ............................................... SUCCESS [19.822s]<br/></span><span class="compile-data">[INFO] bytecode .............................................. SUCCESS [43.522s]<br/></span><span class="compile-data">[INFO] core .................................................. SUCCESS [4:11.890s]<br/></span><span class="compile-data">[INFO] alignment ............................................. SUCCESS [44.522s]<br/></span><span class="compile-data">[INFO] blast ................................................. SUCCESS [1:17.531s]<br/></span><span class="compile-data">[INFO] biojava3-structure .................................... SUCCESS [8:09.397s]<br/></span><span class="compile-data">[INFO] das ................................................... SUCCESS [1:12.949s]<br/></span><span class="compile-data">[INFO] sequence .............................................. SUCCESS [16.823s]<br/></span><span class="compile-data">[INFO] sequence-core ......................................... SUCCESS [46.328s]<br/></span><span class="compile-data">[INFO] sequence-rna .......................................... SUCCESS [27.946s]<br/></span><span class="compile-data">[INFO] sequence-biosql ....................................... SUCCESS [46.370s]<br/></span><span class="compile-data">[INFO] sequence-fasta ........................................ SUCCESS [28.420s]<br/></span><span class="compile-data">[INFO] sequence-blastxml ..................................... SUCCESS [41.663s]<br/></span><span class="compile-data">[INFO] sequencing ............................................ SUCCESS [48.318s]<br/></span><span class="compile-data">[INFO] phylo ................................................. SUCCESS [46.870s]<br/></span><span class="compile-data">[INFO] biosql ................................................ SUCCESS [50.148s]<br/></span><span class="compile-data">[INFO] gui ................................................... SUCCESS [56.724s]<br/></span><span class="compile-data">[INFO] biojava3-core ......................................... SUCCESS [59.994s]<br/></span><span class="compile-data">[INFO] biojava3-phylo ........................................ SUCCESS [45.063s]<br/></span><span class="compile-data">[INFO] biojava3-structure-gui ................................ SUCCESS [1:02.407s]<br/></span><span class="compile-data">[INFO] biojava3-alignment .................................... SUCCESS [52.054s]<br/></span><span class="compile-data">[INFO] biojava3-genome ....................................... SUCCESS [49.626s]<br/></span><span class="compile-data">[INFO] biojava3-protmod ...................................... SUCCESS [20:11.769s]<br/></span><span class="compile-data">[INFO] biojava3-ws ........................................... SUCCESS [42.249s]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] BUILD SUCCESSFUL<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Total time: 48 minutes 53 seconds<br/></span><span class="compile-data">[INFO] Finished at: Wed Jul 28 17:37:33 PDT 2010<br/></span><span class="compile-data">[INFO] Final Memory: 224M/1524M<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
</table>
</p>
<p></p>
<p></p>
<p></p>
<p></p>
<p></p>
<p>
<table xmlns:lxslt="http://xml.apache.org/xslt" align="center" cellpadding="2" cellspacing="0" border="0" width="98%">
<tr>
<td class="unittests-sectionheader" colspan="4">
Unit Tests: (0)
</td>
</tr>
<tr>
<td colspan="2" class="unittests-data">
No Tests Run
</td>
</tr>
<tr>
<td colspan="2" class="unittests-error">
This project doesn't have any tests
</td>
</tr>
<tr>
<td>
<table align="center" cellpadding="2" cellspacing="0" border="0" width="98%"></table>
</td>
</tr>
<tr></tr>
<tr>
<td colspan="2"> </td>
</tr>
</table>
</p>
<p></p>
<p>
<table align="center" cellpadding="2" cellspacing="1" border="0" width="98%">
<tr>
<td class="modifications-sectionheader" colspan="6">
Modifications since last successful build:
(8)
</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSequencePair.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/test/java/org/biojava3/alignment/FractionalSimilarityScorerTest.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/main/java/org/biojava3/alignment/template/PairwiseSequenceScorer.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookMSAProfiler.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/test/java/org/biojava3/alignment/FractionalIdentityScorerTest.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/main/java/org/biojava3/alignment/FractionalSimilarityScorer.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/main/java/org/biojava3/alignment/template/PairwiseSequenceAligner.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">Mark Chapman</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-alignment/src/main/java/org/biojava3/alignment/FractionalIdentityScorer.java</td>
<td class="modifications-data">8156</td>
<td class="modifications-data">2010-07-28T23:05:27</td>
<td class="modifications-data">improvements to memory usage during multiple sequence alignment</td>
</tr>
</table>
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