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View results here -> <a href="http://emmy.rcsb.org:8080/cruisecontrol/buildresults/biojava-svn?log=log20101225011513Lbuild.143">http://emmy.rcsb.org:8080/cruisecontrol/buildresults/biojava-svn?log=log20101225011513Lbuild.143</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.143
</th>
</tr>
<tr>
<th>Date of build:</th>
<td>2010-12-25T09:15:13</td>
</tr>
<tr>
<th>Time to build:</th>
<td>12 minute(s) 56 second(s)</td>
</tr>
<tr>
<th>Last changed:</th>
<td>2010-12-25T08:54:54</td>
</tr>
<tr>
<th>Last log entry:</th>
<td>working around the no-download chem comp provider.</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] biojava3-core<br/></span><span class="compile-data">[INFO] biojava3-phylo<br/></span><span class="compile-data">[INFO] biojava3-alignment<br/></span><span class="compile-data">[INFO] biojava3-structure<br/></span><span class="compile-data">[INFO] biojava3-structure-gui<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-beta5-SNAPSHOT/biojava-3.0-beta5-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]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-beta5-SNAPSHOT/biojava-3.0-beta5-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-beta5-SNAPSHOT/biojava-3.0-beta5-SNAPSHOT.pom<br/></span><span class="compile-data">8K uploaded (biojava-3.0-beta5-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:biojava'<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-beta5-SNAPSHOT'<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 124 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 6 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 13 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 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: 0.101 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.DNATest<br/></span><span class="compile-data">Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.MultipleSequenceAlignmentTest<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.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.compound.AmbiguityDNACompoundTest<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.biojava3.core.sequence.SequenceViewTest<br/></span><span class="compile-data">Tests run: 3, 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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.611 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: 0.006 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: 0.012 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 51, 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-beta5-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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-beta5-SNAPSHOT/biojava3-core-3.0-beta5-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-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.7:javadoc' has not be previously called for the project:
'org.biojava:biojava3-structure:jar:3.0-beta5-SNAPSHOT'. Trying to invoke it...<br/></span><span class="compile-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-structure/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-data">[INFO] <br/></span><span class="compile-data">209 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/ArrayListSequenceReader.java:225:
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/storage/ArrayListSequenceReader.java:216:
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/storage/ArrayListSequenceReader.java:103:
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/storage/ArrayListSequenceReader.java:112:
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/storage/ArrayListSequenceReader.java:162:
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/storage/ArrayListSequenceReader.java:121:
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/storage/ArrayListSequenceReader.java:233:
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/storage/ArrayListSequenceReader.java:130:
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/storage/ArrayListSequenceReader.java:138:
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/storage/ArrayListSequenceReader.java:81:
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/storage/ArrayListSequenceReader.java:93:
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/storage/ArrayListSequenceReader.java:208:
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/storage/ArrayListSequenceReader.java:146:
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/storage/SequenceAsStringHelper.java:28:
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/storage/SingleCompoundSequenceReader.java:144:
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:152:
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:152:
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/CDSComparator.java:38: 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/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain: reference not found: http://www.sequenceontology.org/gff3.shtml<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: 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/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "58" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "126" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:62: 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/CDSSequence.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/CDSSequence.java:82: warning
- Tag @linkplain: reference not found: http://www.sequenceontology.org/gff3.shtml<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain: reference not found: http://biowiki.org/~yam/bioe131/GFF.ppt<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132:
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/ChromosomeSequence.java:144:
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/ChromosomeSequence.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/ChromosomeSequence.java:114:
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/ChromosomeSequence.java:132:
warning - @param argument "begin" 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/ChromosomeSequence.java:132:
warning - @param argument "end" 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/DNASequence.java:128: 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/DNASequence.java:98: 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/DNASequence.java:116: 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/DNASequence.java:107: 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:218: 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:182: 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:149: 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:235: 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:243: 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:75: 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:253: 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:118: 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:126: 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:199: 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:164: 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:135: 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:63: 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/MultipleSequenceAlignment.java:81:
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/MultipleSequenceAlignment.java:90:
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/MultipleSequenceAlignment.java:100:
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/MultipleSequenceAlignment.java:113:
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/MultipleSequenceAlignment.java:123:
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/MultipleSequenceAlignment.java:132:
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/MultipleSequenceAlignment.java:68:
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/MultipleSequenceAlignment.java:176:
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/MultipleSequenceAlignment.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/MultipleSequenceAlignment.java:152:
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/RNASequence.java:103: 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/RNASequence.java:95: 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/RNASequence.java:111: 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/RNASequence.java:122: 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/RNASequence.java:85: 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:596:
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:99:
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:87:
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:185:
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:129:
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:199:
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:208:
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:72:
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:226:
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:241:
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/features/AbstractFeature.java:143:
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/features/FeatureInterface.java:45:
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/features/AbstractFeature.java:67:
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/features/AbstractFeature.java:134:
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/features/FeatureInterface.java:31:
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/features/AbstractFeature.java:106:
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/features/AbstractFeature.java:87:
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/features/FeatureInterface.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/features/FeatureInterface.java:122:
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/features/FeatureInterface.java:129:
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/features/FeatureInterface.java:53:
warning - @return tag cannot be used in method with void return type.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/features/FeaturesKeyWordInterface.java:39:
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/loader/SequenceFileProxyLoader.java:286:
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/loader/SequenceFileProxyLoader.java:277:
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/loader/SequenceFileProxyLoader.java:219:
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/loader/SequenceFileProxyLoader.java:149:
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/loader/SequenceFileProxyLoader.java:255:
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/loader/SequenceFileProxyLoader.java:161:
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/loader/SequenceFileProxyLoader.java:295:
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/loader/SequenceFileProxyLoader.java:173:
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/loader/SequenceFileProxyLoader.java:140:
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/loader/SequenceFileProxyLoader.java:195:
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/loader/SequenceFileProxyLoader.java:206:
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/loader/SequenceFileProxyLoader.java:233:
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/loader/SequenceFileProxyLoader.java:244:
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/loader/SequenceFileProxyLoader.java:184:
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/loader/UniprotProxySequenceReader.java:242:
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/loader/UniprotProxySequenceReader.java:233:
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/loader/UniprotProxySequenceReader.java:182:
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/loader/UniprotProxySequenceReader.java:143:
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/loader/UniprotProxySequenceReader.java:225:
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/loader/UniprotProxySequenceReader.java:443:
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/loader/UniprotProxySequenceReader.java:382:
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/loader/UniprotProxySequenceReader.java:151:
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/loader/UniprotProxySequenceReader.java:190:
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/loader/UniprotProxySequenceReader.java:422:
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/loader/UniprotProxySequenceReader.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/loader/UniprotProxySequenceReader.java:134:
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/loader/UniprotProxySequenceReader.java:402:
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/loader/UniprotProxySequenceReader.java:175:
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/loader/UniprotProxySequenceReader.java:201:
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/loader/UniprotProxySequenceReader.java:211:
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/loader/UniprotProxySequenceReader.java:218:
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/loader/UniprotProxySequenceReader.java:168:
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/location/LocationHelper.java:59:
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/location/LocationHelper.java:122:
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/location/template/Location.java:78:
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:176:
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:102:
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/DNASequenceCreator.java:80:
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/template/SequenceCreatorInterface.java:55:
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/DNASequenceCreator.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/template/SequenceCreatorInterface.java:49:
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/DNASequenceCreator.java:60:
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/template/SequenceCreatorInterface.java:42:
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:88:
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:59:
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:101:
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:86:
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:54:
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: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/template/SequenceParserInterface.java:39:
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:97:
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/FileProxyProteinSequenceCreator.java:96:
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/FileProxyProteinSequenceCreator.java:86:
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/FileProxyProteinSequenceCreator.java:72:
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/template/FastaHeaderFormatInterface.java:38:
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/IUPACParser.java:273:
warning - @param argument "nucleotides" 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/ProteinSequenceCreator.java:67:
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/ProteinSequenceCreator.java:80:
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/ProteinSequenceCreator.java:58:
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/RNASequenceCreator.java:58:
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/RNASequenceCreator.java:49:
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/RNASequenceCreator.java:40:
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/util/IOUtils.java:196:
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:587:
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:525:
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:534:
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:344:
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:327:
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:307:
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:400:
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:543:
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:552:
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:560:
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:516:
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:507:
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:570:
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:167:
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:578:
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:140:
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:158:
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:190:
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:327:
warning - @param argument "featureType" 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:465:
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/AbstractSequence.java:507:
warning - @param argument "begin" 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:507:
warning - @param argument "end" 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:237:
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:156:
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:144:
warning - @param argument "writer" 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:237:
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:39:
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:62:
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:62:
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:62:
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:62:
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:175:
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:74:
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:74:
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:175:
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:39:
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:175:
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:237:
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:237:
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:237:
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:39:
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:39:
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:175:
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:152:
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:237:
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:39:
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:175:
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-beta5-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 6 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 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: 0.106 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.DNATest<br/></span><span class="compile-data">Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.MultipleSequenceAlignmentTest<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.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.compound.AmbiguityDNACompoundTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava3.core.sequence.SequenceViewTest<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.biojava3.core.sequence.TranslationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.635 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: 0.006 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: 0.011 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 51, 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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-beta5-SNAPSHOT/biojava3-core-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-beta5-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-beta5-SNAPSHOT/biojava3-core-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0-beta5-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0-beta5-SNAPSHOT/biojava3-core-3.0-beta5-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-beta5-SNAPSHOT/biojava3-core-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">246K uploaded (biojava3-core-3.0-beta5-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-core:3.0-beta5-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-core 3.0-beta5-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-beta5-SNAPSHOT/biojava3-core-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">185K uploaded (biojava3-core-3.0-beta5-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-beta5-SNAPSHOT/biojava3-core-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">1466K uploaded (biojava3-core-3.0-beta5-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: 0.047 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-beta5-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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-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-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-structure/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-data">[INFO] <br/></span><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-beta5-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: 0.047 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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-beta5-SNAPSHOT-sources.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0-beta5-SNAPSHOT-javadoc.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-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-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">57K uploaded (biojava3-phylo-3.0-beta5-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-beta5-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-phylo 3.0-beta5-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-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">50K uploaded (biojava3-phylo-3.0-beta5-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-beta5-SNAPSHOT/biojava3-phylo-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">102K uploaded (biojava3-phylo-3.0-beta5-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 50 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 19 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: 0.147 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: 0.053 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: 0.018 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.SimpleGapPenaltyTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 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: 0.046 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileProfileAlignerTest<br/></span><span class="compile-data">Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 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: 0.01 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.NeedlemanWunschTest<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileTest<br/></span><span class="compile-data">Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.076 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SmithWatermanTest<br/></span><span class="compile-data">Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.routines.GuanUberbacherTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 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: 0.034 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 210, Failures: 0, Errors: 0, Skipped: 3<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-beta5-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-beta5-SNAPSHOT.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-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-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-structure/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-beta5-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: 0.147 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: 0.052 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: 0.018 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: 0.075 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: 0.009 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: 0.046 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileProfileAlignerTest<br/></span><span class="compile-data">Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 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: 0.01 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.NeedlemanWunschTest<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SimpleProfileTest<br/></span><span class="compile-data">Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.076 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.SmithWatermanTest<br/></span><span class="compile-data">Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec<br/></span><span class="compile-data">Running org.biojava3.alignment.routines.GuanUberbacherTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 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: 0.034 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 210, Failures: 0, Errors: 0, Skipped: 3<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-beta5-SNAPSHOT.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-beta5-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0-beta5-SNAPSHOT-javadoc.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-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-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">100K uploaded (biojava3-alignment-3.0-beta5-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-beta5-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-beta5-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-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">87K uploaded (biojava3-alignment-3.0-beta5-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-beta5-SNAPSHOT/biojava3-alignment-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">625K uploaded (biojava3-alignment-3.0-beta5-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/biojava3-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 54 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 196 source files to /opt/cruise/projects/biojava-svn/biojava3-structure/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 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 49 source files to /opt/cruise/projects/biojava-svn/biojava3-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/biojava3-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: 0.591 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: 0.754 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructurePairAlignerTest<br/></span><span class="compile-data">Dec 25, 2010 1:18:48 AM 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">Dec 25, 2010 1:18:48 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: Not all sites have been properly described in the PDB 1TAP header - some Sites will not be present in the Structure<br/></span><span class="compile-data">Dec 25, 2010 1:18:48 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: [] | [AC1, AC2]<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.074 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: 0.022 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: 4.966 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: 0.064 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: 0.391 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: 0.004 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: 0.249 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">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.284 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.ResidueNumberTest<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.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: 23.985 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.fatcat.FlipAFPChainTest<br/></span><span class="compile-data"> 1 20<br/></span><span class="compile-data"> 45 LLYPPWDKNFTENDLLVRIG 64<br/></span><span class="compile-data"> .| | | .|| .||<br/></span><span class="compile-data"> 75 VLVGPTPVNIIGRNLLTQIG 94<br/></span><span class="compile-data">nr aligned positions:20 20<br/></span><span class="compile-data">LLYPPWDKNFTENDLLVRIG<br/></span><span class="compile-data">:| | | :|| :||<br/></span><span class="compile-data">VLVGPTPVNIIGRNLLTQIG<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.269 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.FlipAFPChainTest<br/></span><span class="compile-data">mismatch in line: 101<br/></span><span class="compile-data">line1: <shift x="-6.029" y="-24.374<br/></span><span class="compile-data">line2: <shift x="-6.029" y="-24.373<br/></span><span class="compile-data">mismatch at position 32 c1: 4 3<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.359 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: 9.349 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: 0.487 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.Test1a4w<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 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: 4.167 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: 13.602 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.PDBFileParserTest<br/></span><span class="compile-data">Dec 25, 2010 1:20:00 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: No chains to link Site Groups with - Sites will not be present in the Structure<br/></span><span class="compile-data">Dec 25, 2010 1:20:00 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: No chains to link Site Groups with - Sites will not be present in the Structure<br/></span><span class="compile-data">Dec 25, 2010 1:20:00 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: No chains to link Site Groups with - Sites will not be present in the Structure<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.ChemCompTest<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">downloading http://www.rcsb.org/pdb/files/ligand/MEA.cif<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.SiteTest<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.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.Test4hhb<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.712 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.TestOutputStrings<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 31.966 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.HetatomImplTest<br/></span><span class="compile-data">testSetResidueNumberUsage<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestAltLocs<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.structure.align.fatcat.AFPChainSerialisationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.881 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: 0.052 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: 0.177 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 85, 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-structure/target/biojava3-structure-3.0-beta5-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-structure/target/biojava3-structure-3.0-beta5-SNAPSHOT.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-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-structure/target/biojava3-structure-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-data">[INFO] <br/></span><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/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java:407:
warning - @param argument "flag" is not a parameter name.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0-beta5-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 54 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/biojava3-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: 0.59 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: 0.762 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.StructurePairAlignerTest<br/></span><span class="compile-data">Dec 25, 2010 1:21:07 AM 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">Dec 25, 2010 1:21:07 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: Not all sites have been properly described in the PDB 1TAP header - some Sites will not be present in the Structure<br/></span><span class="compile-data">Dec 25, 2010 1:21:07 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: [] | [AC1, AC2]<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.075 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: 0.023 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: 5.01 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: 0.065 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: 0.399 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: 0.004 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: 0.255 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">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.276 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.ResidueNumberTest<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.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: 24.091 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: 0.039 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.FlipAFPChainTest<br/></span><span class="compile-data"> 1 20<br/></span><span class="compile-data"> 45 LLYPPWDKNFTENDLLVRIG 64<br/></span><span class="compile-data"> .| | | .|| .||<br/></span><span class="compile-data"> 75 VLVGPTPVNIIGRNLLTQIG 94<br/></span><span class="compile-data">nr aligned positions:20 20<br/></span><span class="compile-data">LLYPPWDKNFTENDLLVRIG<br/></span><span class="compile-data">:| | | :|| :||<br/></span><span class="compile-data">VLVGPTPVNIIGRNLLTQIG<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.316 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.FlipAFPChainTest<br/></span><span class="compile-data">mismatch in line: 101<br/></span><span class="compile-data">line1: <shift x="-6.029" y="-24.374<br/></span><span class="compile-data">line2: <shift x="-6.029" y="-24.373<br/></span><span class="compile-data">mismatch at position 32 c1: 4 3<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.364 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: 9.341 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: 0.494 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.Test1a4w<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 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: 4.218 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: 13.6 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.PDBFileParserTest<br/></span><span class="compile-data">Dec 25, 2010 1:22:19 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: No chains to link Site Groups with - Sites will not be present in the Structure<br/></span><span class="compile-data">Dec 25, 2010 1:22:19 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: No chains to link Site Groups with - Sites will not be present in the Structure<br/></span><span class="compile-data">Dec 25, 2010 1:22:19 AM org.biojava.bio.structure.io.PDBFileParser linkSitesToGroups<br/></span><span class="compile-data">WARNING: No chains to link Site Groups with - Sites will not be present in the Structure<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.ChemCompTest<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">downloading http://www.rcsb.org/pdb/files/ligand/MEA.cif<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.biojava.bio.structure.SiteTest<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.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.Test4hhb<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.711 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.TestOutputStrings<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 31.975 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.HetatomImplTest<br/></span><span class="compile-data">testSetResidueNumberUsage<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.TestAltLocs<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec<br/></span><span class="compile-data">Running org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.855 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: 0.051 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: 0.175 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 85, 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-structure/target/biojava3-structure-3.0-beta5-SNAPSHOT.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0-beta5-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0-beta5-SNAPSHOT-javadoc.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-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-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">605K uploaded (biojava3-structure-3.0-beta5-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'<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-beta5-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-structure 3.0-beta5-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-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">534K uploaded (biojava3-structure-3.0-beta5-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-beta5-SNAPSHOT/biojava3-structure-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">2199K uploaded (biojava3-structure-3.0-beta5-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/biojava3-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><span class="compile-data">[INFO] snapshot org.biojava:biojava:3.0-alpha2-SNAPSHOT: checking for updates from biojava-maven-repo<br/></span><span class="compile-data">[INFO] snapshot org.biojava:biojava:3.0-alpha2-SNAPSHOT: checking for updates from maven2-repository.dev.java.net<br/></span><span class="compile-data">[INFO] snapshot org.biojava:biojava:3.0-alpha2-SNAPSHOT: checking for updates from maven-repository.dev.java.net<br/></span><span class="compile-data">Downloading: http://www.biojava.org/download/maven//org/biojava/biojava/3.0-alpha2-SNAPSHOT/biojava-3.0-alpha2-SNAPSHOT.pom<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/biojava3-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/biojava3-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/biojava3-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/biojava3-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: 0.063 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: 0.004 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/biojava3-structure-gui/target/biojava3-structure-gui-3.0-beta5-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-structure-gui/target/biojava3-structure-gui-3.0-beta5-SNAPSHOT.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-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-structure-gui/target/biojava3-structure-gui-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0-beta5-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/biojava3-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/biojava3-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/biojava3-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/biojava3-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: 0.056 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: 0.014 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/biojava3-structure-gui/target/biojava3-structure-gui-3.0-beta5-SNAPSHOT.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0-beta5-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0-beta5-SNAPSHOT-javadoc.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-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-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">243K uploaded (biojava3-structure-gui-3.0-beta5-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-beta5-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-structure-gui 3.0-beta5-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-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">157K uploaded (biojava3-structure-gui-3.0-beta5-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-beta5-SNAPSHOT/biojava3-structure-gui-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">847K uploaded (biojava3-structure-gui-3.0-beta5-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><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/testoutput (includes = [**/volvox_all.faa],
excludes = [])<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 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] Copying 9 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/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.GeneFeatureHelperTest<br/></span><span class="compile-data">Gene EDEN found at ctgA 1050 9000 POSITIVE<br/></span><span class="compile-data">Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE<br/></span><span class="compile-data">Dec 25, 2010 1:25:13 AM org.biojava3.genome.parsers.gff.GFF3Reader read<br/></span><span class="compile-data">INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3<br/></span><span class="compile-data">Note [protein kinase]<br/></span><span class="compile-data">Dec 25, 2010 1:25:13 AM org.biojava3.genome.parsers.gff.GFF3Reader read<br/></span><span class="compile-data">INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3<br/></span><span class="compile-data">Dec 25, 2010 1:25:13 AM org.biojava3.genome.parsers.gff.GFF3Reader read<br/></span><span class="compile-data">INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.709 sec<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: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 6, 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-beta5-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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-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-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-error-data">[ERROR] Error fetching link: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/apidocs/package-list. Ignored it.<br/></span><span class="compile-data">[INFO] <br/></span><span class="compile-data">4 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:180: 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/GeneFeatureHelper.java:329: 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-beta5-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 10 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.GeneFeatureHelperTest<br/></span><span class="compile-data">Gene EDEN found at ctgA 1050 9000 POSITIVE<br/></span><span class="compile-data">Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE<br/></span><span class="compile-data">Dec 25, 2010 1:25:21 AM org.biojava3.genome.parsers.gff.GFF3Reader read<br/></span><span class="compile-data">INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3<br/></span><span class="compile-data">Note [protein kinase]<br/></span><span class="compile-data">Dec 25, 2010 1:25:21 AM org.biojava3.genome.parsers.gff.GFF3Reader read<br/></span><span class="compile-data">INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3<br/></span><span class="compile-data">Dec 25, 2010 1:25:21 AM org.biojava3.genome.parsers.gff.GFF3Reader read<br/></span><span class="compile-data">INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.718 sec<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: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 6, 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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-beta5-SNAPSHOT-sources.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0-beta5-SNAPSHOT-javadoc.jar to
/home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-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-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">58K uploaded (biojava3-genome-3.0-beta5-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] 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-beta5-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for biojava3-genome 3.0-beta5-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-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">40K uploaded (biojava3-genome-3.0-beta5-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-beta5-SNAPSHOT/biojava3-genome-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">243K uploaded (biojava3-genome-3.0-beta5-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 22 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 4 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.structure.ProteinModificationRegistryTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.463 sec<br/></span><span class="compile-data">Running org.biojava3.protmod.structure.ProteinModificationParserTest<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">downloading http://www.rcsb.org/pdb/files/ligand/PRO.cif<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.598 sec<br/></span><span class="compile-data">Running org.biojava3.protmod.structure.ModifiedCompoundSerializationTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.689 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/biojava3-protmod/target/biojava3-protmod-3.0-beta5-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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-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-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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] <br/></span><span class="compile-data">18 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/Component.java:143: warning
- @param argument "pdbccIds" 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 "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/ProteinModificationRegistry.java:184:
warning - @param argument "mod" 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/structure/ModifiedCompound.java:82:
warning - Tag @see: can't find getLinkedGroupPairs in org.biojava3.protmod.structure.ModifiedCompound<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:88:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:54:
warning - Tag @link: reference not found: ProteinModificationBean<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:88:
warning - @return tag cannot be used in method with void return type.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:96:
warning - Tag @link: reference not found: addGroup<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompoundImpl.java:69:
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/structure/ModifiedCompound.java:54:
warning - Tag @link: reference not found: ProteinModificationBean<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:96:
warning - Tag @link: reference not found: addGroup<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ProteinModificationIdentifier.java:91:
warning - @param argument "recordUnidentifiableAtomLinkages" 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/structure/StructureUtil.java:285:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-beta5-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.structure.ProteinModificationRegistryTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.464 sec<br/></span><span class="compile-data">Running org.biojava3.protmod.structure.ProteinModificationParserTest<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">creating directory /tmpchemcomp<br/></span><span class="compile-data">downloading http://www.rcsb.org/pdb/files/ligand/PRO.cif<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.516 sec<br/></span><span class="compile-data">Running org.biojava3.protmod.structure.ModifiedCompoundSerializationTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.684 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/biojava3-protmod/target/biojava3-protmod-3.0-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-beta5-SNAPSHOT-sources.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protmod/target/biojava3-protmod-3.0-beta5-SNAPSHOT-javadoc.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-protmod/3.0-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-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-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">82K uploaded (biojava3-protmod-3.0-beta5-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-beta5-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-beta5-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-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">62K uploaded (biojava3-protmod-3.0-beta5-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-beta5-SNAPSHOT/biojava3-protmod-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">243K uploaded (biojava3-protmod-3.0-beta5-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 7 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-beta5-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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-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-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <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-beta5-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-beta5-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-beta5-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0-beta5-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-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-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-SNAPSHOT.jar<br/></span><span class="compile-data">13K uploaded (biojava3-ws-3.0-beta5-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-beta5-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-beta5-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-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-SNAPSHOT-sources.jar<br/></span><span class="compile-data">13K uploaded (biojava3-ws-3.0-beta5-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-beta5-SNAPSHOT/biojava3-ws-3.0-beta5-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">94K uploaded (biojava3-ws-3.0-beta5-SNAPSHOT-javadoc.jar)<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: [javadoc:aggregate] (aggregator-style)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Preparing javadoc:aggregate<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-core<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-phylo<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-alignment<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-structure<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<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] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-genome<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-protmod<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava3-ws<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code>
instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:aggregate {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] <br/></span><span class="compile-data">234 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/ArrayListSequenceReader.java:225:
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/storage/ArrayListSequenceReader.java:216:
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/storage/ArrayListSequenceReader.java:103:
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/storage/ArrayListSequenceReader.java:112:
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/storage/ArrayListSequenceReader.java:162:
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/storage/ArrayListSequenceReader.java:121:
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/storage/ArrayListSequenceReader.java:233:
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/storage/ArrayListSequenceReader.java:130:
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/storage/ArrayListSequenceReader.java:138:
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/storage/ArrayListSequenceReader.java:81:
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/storage/ArrayListSequenceReader.java:93:
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/storage/ArrayListSequenceReader.java:208:
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/storage/ArrayListSequenceReader.java:146:
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/storage/SequenceAsStringHelper.java:28:
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/storage/SingleCompoundSequenceReader.java:144:
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:152:
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:152:
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/CDSComparator.java:38: 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/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning
- Tag @linkplain: reference not found: http://www.sequenceontology.org/gff3.shtml<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: 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/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "58" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "126" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt"<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:62: 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/CDSSequence.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/CDSSequence.java:82: warning
- Tag @linkplain: reference not found: http://www.sequenceontology.org/gff3.shtml<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:82: warning
- Tag @linkplain: reference not found: http://biowiki.org/~yam/bioe131/GFF.ppt<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132:
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/ChromosomeSequence.java:144:
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/ChromosomeSequence.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/ChromosomeSequence.java:114:
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/ChromosomeSequence.java:132:
warning - @param argument "begin" 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/ChromosomeSequence.java:132:
warning - @param argument "end" 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/DNASequence.java:128: 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/DNASequence.java:98: 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/DNASequence.java:116: 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/DNASequence.java:107: 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:218: 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:182: 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:149: 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:235: 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:243: 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:75: 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:253: 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:118: 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:126: 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:199: 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:164: 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:135: 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:63: 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/MultipleSequenceAlignment.java:81:
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/MultipleSequenceAlignment.java:90:
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/MultipleSequenceAlignment.java:100:
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/MultipleSequenceAlignment.java:113:
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/MultipleSequenceAlignment.java:123:
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/MultipleSequenceAlignment.java:132:
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/MultipleSequenceAlignment.java:68:
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/MultipleSequenceAlignment.java:176:
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/MultipleSequenceAlignment.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/MultipleSequenceAlignment.java:152:
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/RNASequence.java:103: 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/RNASequence.java:95: 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/RNASequence.java:111: 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/RNASequence.java:122: 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/RNASequence.java:85: 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:596:
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:99:
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:87:
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:185:
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:129:
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:199:
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:208:
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:72:
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:226:
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:241:
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/features/AbstractFeature.java:143:
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/features/FeatureInterface.java:45:
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/features/AbstractFeature.java:67:
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/features/AbstractFeature.java:134:
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/features/FeatureInterface.java:31:
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/features/AbstractFeature.java:106:
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/features/AbstractFeature.java:87:
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/features/FeatureInterface.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/features/FeatureInterface.java:122:
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/features/FeatureInterface.java:129:
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/features/FeatureInterface.java:53:
warning - @return tag cannot be used in method with void return type.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/features/FeaturesKeyWordInterface.java:39:
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/loader/SequenceFileProxyLoader.java:286:
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/loader/SequenceFileProxyLoader.java:277:
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/loader/SequenceFileProxyLoader.java:219:
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/loader/SequenceFileProxyLoader.java:149:
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/loader/SequenceFileProxyLoader.java:255:
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/loader/SequenceFileProxyLoader.java:161:
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/loader/SequenceFileProxyLoader.java:295:
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/loader/SequenceFileProxyLoader.java:173:
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/loader/SequenceFileProxyLoader.java:140:
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/loader/SequenceFileProxyLoader.java:195:
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/loader/SequenceFileProxyLoader.java:206:
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/loader/SequenceFileProxyLoader.java:233:
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/loader/SequenceFileProxyLoader.java:244:
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/loader/SequenceFileProxyLoader.java:184:
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/loader/UniprotProxySequenceReader.java:242:
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/loader/UniprotProxySequenceReader.java:233:
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/loader/UniprotProxySequenceReader.java:182:
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/loader/UniprotProxySequenceReader.java:143:
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/loader/UniprotProxySequenceReader.java:225:
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/loader/UniprotProxySequenceReader.java:443:
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/loader/UniprotProxySequenceReader.java:382:
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/loader/UniprotProxySequenceReader.java:151:
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/loader/UniprotProxySequenceReader.java:190:
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/loader/UniprotProxySequenceReader.java:422:
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/loader/UniprotProxySequenceReader.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/loader/UniprotProxySequenceReader.java:134:
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/loader/UniprotProxySequenceReader.java:402:
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/loader/UniprotProxySequenceReader.java:175:
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/loader/UniprotProxySequenceReader.java:201:
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/loader/UniprotProxySequenceReader.java:211:
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/loader/UniprotProxySequenceReader.java:218:
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/loader/UniprotProxySequenceReader.java:168:
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/location/LocationHelper.java:59:
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/location/LocationHelper.java:122:
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/location/template/Location.java:78:
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:176:
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:102:
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/DNASequenceCreator.java:80:
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/template/SequenceCreatorInterface.java:55:
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/DNASequenceCreator.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/template/SequenceCreatorInterface.java:49:
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/DNASequenceCreator.java:60:
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/template/SequenceCreatorInterface.java:42:
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:88:
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:59:
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:101:
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:86:
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:54:
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: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/template/SequenceParserInterface.java:39:
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:97:
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/FileProxyProteinSequenceCreator.java:96:
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/FileProxyProteinSequenceCreator.java:86:
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/FileProxyProteinSequenceCreator.java:72:
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/template/FastaHeaderFormatInterface.java:38:
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/IUPACParser.java:273:
warning - @param argument "nucleotides" 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/ProteinSequenceCreator.java:67:
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/ProteinSequenceCreator.java:80:
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/ProteinSequenceCreator.java:58:
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/RNASequenceCreator.java:58:
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/RNASequenceCreator.java:49:
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/RNASequenceCreator.java:40:
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/util/IOUtils.java:196:
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:587:
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:525:
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:534:
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:344:
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:327:
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:307:
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:400:
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:543:
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:552:
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:560:
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:516:
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:507:
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:570:
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:167:
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:578:
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:140:
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:158:
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:190:
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:327:
warning - @param argument "featureType" 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:465:
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/AbstractSequence.java:507:
warning - @param argument "begin" 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:507:
warning - @param argument "end" 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:237:
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:156:
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:144:
warning - @param argument "writer" 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:237:
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:39:
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:62:
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:62:
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:62:
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:62:
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:175:
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:74:
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:74:
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:175:
warning - Tag @link: reference not found: TranslationEngine<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">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java:407:
warning - @param argument "flag" 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/GeneFeatureHelper.java:180: 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/GeneFeatureHelper.java:329: 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">[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/Component.java:143: warning
- @param argument "pdbccIds" 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 "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/ProteinModificationRegistry.java:184:
warning - @param argument "mod" 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/structure/ModifiedCompound.java:82:
warning - Tag @see: can't find getLinkedGroupPairs in org.biojava3.protmod.structure.ModifiedCompound<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:88:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:54:
warning - Tag @link: reference not found: ProteinModificationBean<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:88:
warning - @return tag cannot be used in method with void return type.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:96:
warning - Tag @link: reference not found: addGroup<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-svn/biojava3-protmod/src/main/java/org/biojava3/protmod/structure/ModifiedCompoundImpl.java:69:
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/structure/ModifiedCompound.java:54:
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warning - @param argument "recordUnidentifiableAtomLinkages" 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/structure/StructureUtil.java:285:
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/transcription/Table.java:39:
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warning - Tag @link: reference not found: TranslationEngine<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 [21.661s]<br/></span><span class="compile-data">[INFO] biojava3-core ......................................... SUCCESS [1:18.630s]<br/></span><span class="compile-data">[INFO] biojava3-phylo ........................................ SUCCESS [43.064s]<br/></span><span class="compile-data">[INFO] biojava3-alignment .................................... SUCCESS [57.639s]<br/></span><span class="compile-data">[INFO] biojava3-structure .................................... SUCCESS [5:26.467s]<br/></span><span class="compile-data">[INFO] biojava3-structure-gui ................................ SUCCESS [1:03.646s]<br/></span><span class="compile-data">[INFO] biojava3-genome ....................................... SUCCESS [46.668s]<br/></span><span class="compile-data">[INFO] biojava3-protmod ...................................... SUCCESS [1:04.615s]<br/></span><span class="compile-data">[INFO] biojava3-ws ........................................... SUCCESS [47.175s]<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: 12 minutes 54 seconds<br/></span><span class="compile-data">[INFO] Finished at: Sat Dec 25 01:28:10 PST 2010<br/></span><span class="compile-data">[INFO] Final Memory: 134M/1876M<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
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<td class="unittests-sectionheader" colspan="4">
Unit Tests: (0)
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<td colspan="2" class="unittests-data">
No Tests Run
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<td colspan="2" class="unittests-error">
This project doesn't have any tests
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<p>
<table align="center" cellpadding="2" cellspacing="1" border="0" width="98%">
<tr>
<td class="modifications-sectionheader" colspan="6">
Modifications since last successful build:
(26)
</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/test/java/org/biojava/bio/structure/ChemCompTest.java</td>
<td class="modifications-data">8645</td>
<td class="modifications-data">2010-12-25T08:54:54</td>
<td class="modifications-data">working around the no-download chem comp provider.</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/test/java/org/biojava/bio/structure/ChemCompTest.java</td>
<td class="modifications-data">8644</td>
<td class="modifications-data">2010-12-24T13:07:04</td>
<td class="modifications-data">cleanup</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java</td>
<td class="modifications-data">8643</td>
<td class="modifications-data">2010-12-24T08:26:14</td>
<td class="modifications-data">user now explicitely has to request download of big file...</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">added</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/test/java/org/biojava/bio/structure/ChemCompTest.java</td>
<td class="modifications-data">8642</td>
<td class="modifications-data">2010-12-24T08:20:06</td>
<td class="modifications-data">new junit test for checking of correct loading of chem comps</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/chem/ResidueType.java</td>
<td class="modifications-data">8641</td>
<td class="modifications-data">2010-12-24T08:19:40</td>
<td class="modifications-data">fixing a problem with some chem comp definitions</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/test/resources/volvox_all_reference.faa</td>
<td class="modifications-data">8640</td>
<td class="modifications-data">2010-12-23T13:23:31</td>
<td class="modifications-data">Changed test case reference where stop codons are being returned as * now</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">deleted</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/test/resources/testoutput/volvox_all.faa</td>
<td class="modifications-data">8640</td>
<td class="modifications-data">2010-12-23T13:23:31</td>
<td class="modifications-data">Changed test case reference where stop codons are being returned as * now</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/pom.xml</td>
<td class="modifications-data">8639</td>
<td class="modifications-data">2010-12-22T05:36:29</td>
<td class="modifications-data">updating version nr. of depedencies.</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/SeqRes2AtomAligner.java</td>
<td class="modifications-data">8638</td>
<td class="modifications-data">2010-12-21T23:45:56</td>
<td class="modifications-data">fixing index offset issue</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java</td>
<td class="modifications-data">8637</td>
<td class="modifications-data">2010-12-21T23:44:21</td>
<td class="modifications-data">adding checkPath functionality</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/demo/DemoChangeChemCompProvider.java</td>
<td class="modifications-data">8636</td>
<td class="modifications-data">2010-12-21T23:43:14</td>
<td class="modifications-data">cleanup warning</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">added</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/demo/DemoChangeChemCompProvider.java</td>
<td class="modifications-data">8635</td>
<td class="modifications-data">2010-12-21T23:42:54</td>
<td class="modifications-data">new demo for how to use alternate chem comp providers</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/ReducedChemCompProvider.java</td>
<td class="modifications-data">8634</td>
<td class="modifications-data">2010-12-21T23:42:27</td>
<td class="modifications-data">more javadoc</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/ChemComp.java</td>
<td class="modifications-data">8633</td>
<td class="modifications-data">2010-12-21T23:41:59</td>
<td class="modifications-data">more javadoc</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/ChemCompProvider.java</td>
<td class="modifications-data">8632</td>
<td class="modifications-data">2010-12-21T23:41:42</td>
<td class="modifications-data">more javadoc</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">added</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/AllChemCompProvider.java</td>
<td class="modifications-data">8631</td>
<td class="modifications-data">2010-12-21T23:41:29</td>
<td class="modifications-data">new provider for caching all components in memory</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">andreas</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java</td>
<td class="modifications-data">8630</td>
<td class="modifications-data">2010-12-21T23:40:58</td>
<td class="modifications-data">now with support for download all of the chem comp definitions</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/test/java/org/biojava3/genome/GeneFeatureHelperTest.java</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Reader.java</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/test/resources/volvox_all_genes_exon_uppercase.fna</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/test/resources/volvox_all_reference.faa</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/pom.xml</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/test/resources/testoutput/volvox_all_genes_exon_uppercase.gff3</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/main/java/org/biojava3/genome/query/OutputHitsGFF.java</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
<tr class="modifications-oddrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">hwillis</td>
<td class="modifications-data">/biojava-live/trunk/biojava3-genome/src/main/java/org/biojava3/genome/uniprot/UniprotToFasta.java</td>
<td class="modifications-data">8629</td>
<td class="modifications-data">2010-12-20T21:03:25</td>
<td class="modifications-data">Minor updates</td>
</tr>
</table>
</p>
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