| ||||||
| BUILD COMPLETE - build.436 | |
|---|---|
| Date of build: | 2012-05-15T20:53:05 |
| Time to build: | 13 minute(s) 22 second(s) |
| Last changed: | 2012-05-15T20:45:51 |
| Last log entry: | fix according to S Darnell and P Troshin |
| Build Artifacts |
| Modifications since last successful build: (24) | |||||
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3 | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model0.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model1.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model0.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model2.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model1.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model3.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model2.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model3.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model4.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model4.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model5.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model5.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model6.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model7.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model6.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model8.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model7.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| deleted | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/model9.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model8.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| added | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model9.rec | 9640 | 2012-05-15T20:45:51 | fix according to S Darnell and P Troshin |
| modified | andreas | /biojava-live/trunk/biojava3-protein-disorder/src/main/java/org/biojava3/ronn/ModelLoader.java | 9639 | 2012-05-15T20:45:34 | fix according to S Darnell and P Troshin |
| Initial Messages |
| [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] biojava [INFO] biojava3-core [INFO] biojava3-phylo [INFO] biojava3-sequencing [INFO] biojava3-alignment [INFO] biojava3-structure [INFO] biojava3-structure-gui [INFO] biojava3-genome [INFO] biojava3-modfinder [INFO] biojava3-ws [INFO] biojava3-protein-disorder [INFO] biojava3-aa-prop [INFO] Searching repository for plugin with prefix: 'source'. [INFO] org.apache.maven.plugins: checking for updates from maven2-repository.dev.java.net [INFO] org.apache.maven.plugins: checking for updates from maven-repository.dev.java.net [INFO] org.codehaus.mojo: checking for updates from maven2-repository.dev.java.net [INFO] org.codehaus.mojo: checking for updates from maven-repository.dev.java.net [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/target |
| site:attach-descriptor {execution: default-attach-descriptor} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava/3.0.4-SNAPSHOT/biojava-3.0.4-SNAPSHOT.pom [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code>
instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] Not executing Javadoc as the project is not a Java classpath-capable package |
| site:attach-descriptor {execution: default-attach-descriptor} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava/3.0.4-SNAPSHOT/biojava-3.0.4-SNAPSHOT.pom |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava/3.0.4-SNAPSHOT/biojava-3.0.4-SNAPSHOT.pom 7K uploaded (biojava-3.0.4-SNAPSHOT.pom) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava:3.0.4-SNAPSHOT' [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-core [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-core/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 128 source files to /opt/cruise/projects/biojava-svn/biojava3-core/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 14 source files to /opt/cruise/projects/biojava-svn/biojava3-core/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-core/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.core.sequence.io.FastaReaderTest process Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 sec Running org.biojava3.core.sequence.compound.AmbiguityDNACompoundTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec Running org.biojava3.core.sequence.MultipleSequenceAlignmentTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava3.core.sequence.io.GenericFastaHeaderParserTest parseHeader Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava3.core.sequence.io.FastaWriterTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.core.sequence.location.LocationParserTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec Running org.biojava3.core.sequence.JoiningSequenceReaderTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava3.core.sequence.EditSequenceTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreatorTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.core.sequence.DNATest Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.245 sec Running org.biojava3.core.sequence.SequenceViewTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava3.core.sequence.TranslationTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 sec Running org.biojava3.core.sequence.location.LocationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Results : Tests run: 55, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] 186 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link: reference not found: http://www.sequenceontology.org/gff3.shtml [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "58" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "126" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:564: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link: reference not found: http://www.sequenceontology.org/gff3.shtml [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link: reference not found: http://biowiki.org/~yam/bioe131/GFF.ppt [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:144: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:105: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:114: warning - @return tag has no arguments. [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. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:103: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:95: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:111: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:122: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:85: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:600: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:104: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:92: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:190: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:134: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:204: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:213: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:77: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:231: warning - @param argument "startCodonSequence" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:246: warning - @param argument "stopCodonSequence" is not a parameter name. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @ is an unknown tag. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @ is an unknown tag. [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:74: warning - @ is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:74: warning - @ is an unknown tag. [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 [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:244: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:235: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:109: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:118: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:168: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:127: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:253: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:136: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:144: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:88: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:99: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:227: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:152: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:146: warning - Tag @link: can't find countCompounds(org.biojava3.core.sequence.template.Sequence, C[]) in org.biojava3.core.sequence.template.SequenceMixin [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:96: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:61: warning - @param argument "br" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:115: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:51: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:100: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:69: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:85: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaWriterHelper.java:103: warning - @param argument "dnaSequences" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:96: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:86: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:72: warning - @return tag has no arguments. [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. [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. [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. [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. [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. [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. [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. [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:287: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:278: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:220: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:150: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:256: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:162: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:296: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:174: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:141: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:196: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:207: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:234: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:245: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:185: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:259: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:238: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:183: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:140: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:230: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:466: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:149: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:192: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:446: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:158: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:131: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:424: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:203: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:214: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:222: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:167: warning - @return tag has no arguments. [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. [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java:114: warning - @param argument "<C>" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java:125: warning - @param argument "<C>" is not a parameter name. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:591: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:529: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:538: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:348: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:331: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:311: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:404: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:520: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:574: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:171: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:582: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:144: warning - @param argument "bioBegin" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:162: warning - @param argument "bioEnd" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:194: warning - @param argument "annotation" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:331: warning - @param argument "featureType" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:469: warning - @param argument "species" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @param argument "begin" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @param argument "end" is not a parameter name. [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 [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 [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/util/StringManipulationHelper.java:73: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/util/StringManipulationHelper.java:73: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /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 [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 [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 [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 [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 [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 [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 [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [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 [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 [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 [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-core/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.core.sequence.io.FastaReaderTest process Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec Running org.biojava3.core.sequence.compound.AmbiguityDNACompoundTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec Running org.biojava3.core.sequence.MultipleSequenceAlignmentTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava3.core.sequence.io.GenericFastaHeaderParserTest parseHeader Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava3.core.sequence.io.FastaWriterTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.core.sequence.location.LocationParserTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava3.core.sequence.JoiningSequenceReaderTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava3.core.sequence.EditSequenceTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreatorTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojava3.core.sequence.DNATest Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 sec Running org.biojava3.core.sequence.SequenceViewTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava3.core.sequence.TranslationTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.539 sec Running org.biojava3.core.sequence.location.LocationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Results : Tests run: 55, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-core/target/biojava3-core-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT.jar 257K uploaded (biojava3-core-3.0.4-SNAPSHOT.jar) [INFO] Uploading project information for biojava3-core 3.0.4-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-core:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-core' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT-sources.jar 195K uploaded (biojava3-core-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-core/3.0.4-SNAPSHOT/biojava3-core-3.0.4-SNAPSHOT-javadoc.jar 1524K uploaded (biojava3-core-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-phylo [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-phylo/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 10 source files to /opt/cruise/projects/biojava-svn/biojava3-phylo/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-phylo/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/biojava3-phylo/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.phylo.AppTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec Results : Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] 3 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [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. [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. [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-phylo/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-phylo/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.phylo.AppTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec Results : Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-phylo/target/biojava3-phylo-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT.jar 57K uploaded (biojava3-phylo-3.0.4-SNAPSHOT.jar) [INFO] Uploading project information for biojava3-phylo 3.0.4-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-phylo:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-phylo' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT-sources.jar 50K uploaded (biojava3-phylo-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-phylo/3.0.4-SNAPSHOT/biojava3-phylo-3.0.4-SNAPSHOT-javadoc.jar 116K uploaded (biojava3-phylo-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-sequencing [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-sequencing/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-sequencing/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 19 source files to /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 74 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 13 source files to /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.sequencing.io.fastq.FastqBuilderTest Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec Running org.biojava3.sequencing.io.fastq.FastqTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.sequencing.io.fastq.SolexaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec Running org.biojava3.sequencing.io.fastq.IlluminaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec Running org.biojava3.sequencing.io.fastq.FastqToolsTest Tests run: 28, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec Running org.biojava3.sequencing.io.fastq.FastqVariantTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava3.sequencing.io.fastq.SangerFastqReaderTest Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec Running org.biojava3.sequencing.io.fastq.IlluminaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.sequencing.io.fastq.SolexaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojava3.sequencing.io.fastq.StreamingFastqParserTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava3.sequencing.io.fastq.SangerFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Results : Tests run: 169, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] 1 warning [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-sequencing/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 74 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.sequencing.io.fastq.FastqBuilderTest Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec Running org.biojava3.sequencing.io.fastq.FastqTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.sequencing.io.fastq.SolexaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec Running org.biojava3.sequencing.io.fastq.IlluminaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec Running org.biojava3.sequencing.io.fastq.FastqToolsTest Tests run: 28, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec Running org.biojava3.sequencing.io.fastq.FastqVariantTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava3.sequencing.io.fastq.SangerFastqReaderTest Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec Running org.biojava3.sequencing.io.fastq.IlluminaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.sequencing.io.fastq.SolexaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojava3.sequencing.io.fastq.StreamingFastqParserTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava3.sequencing.io.fastq.SangerFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Results : Tests run: 169, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-sequencing/target/biojava3-sequencing-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT.jar 27K uploaded (biojava3-sequencing-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-sequencing:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-sequencing' [INFO] Uploading project information for biojava3-sequencing 3.0.4-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT-sources.jar 21K uploaded (biojava3-sequencing-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-sequencing/3.0.4-SNAPSHOT/biojava3-sequencing-3.0.4-SNAPSHOT-javadoc.jar 135K uploaded (biojava3-sequencing-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-alignment [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-alignment/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 20 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 55 source files to /opt/cruise/projects/biojava-svn/biojava3-alignment/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 21 source files to /opt/cruise/projects/biojava-svn/biojava3-alignment/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.alignment.FractionalSimilarityScorerTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 sec Running org.biojava3.alignment.SimpleSubstitutionMatrixTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 sec Running org.biojava3.alignment.SimpleProfilePairTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec Running org.biojava3.alignment.GuideTreeTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec Running org.biojava3.alignment.SimpleGapPenaltyTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava3.alignment.SimpleSequencePairTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec Running org.biojava3.alignment.SimpleProfileProfileAlignerTest Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec Running org.biojava3.alignment.FractionalIdentityScorerTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojava3.alignment.NeedlemanWunschTest Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec Running org.biojava3.alignment.SimpleProfileTest Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.089 sec Running org.biojava3.alignment.routines.GuanUberbacherTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec Running org.biojava3.alignment.aaindex.TestAAINDEXLoading Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 sec Running org.biojava3.alignment.SmithWatermanTest Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec Running org.biojava3.alignment.TestDNAAlignment Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.87 sec Running org.biojava3.alignment.SimpleAlignedSequenceTest Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.035 sec Results : Tests run: 215, Failures: 0, Errors: 0, Skipped: 3 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] 1 warning [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 20 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-alignment/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.alignment.FractionalSimilarityScorerTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 sec Running org.biojava3.alignment.SimpleSubstitutionMatrixTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 sec Running org.biojava3.alignment.SimpleProfilePairTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava3.alignment.GuideTreeTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec Running org.biojava3.alignment.SimpleGapPenaltyTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava3.alignment.SimpleSequencePairTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec Running org.biojava3.alignment.SimpleProfileProfileAlignerTest Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec Running org.biojava3.alignment.FractionalIdentityScorerTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojava3.alignment.NeedlemanWunschTest Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec Running org.biojava3.alignment.SimpleProfileTest Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.083 sec Running org.biojava3.alignment.routines.GuanUberbacherTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.biojava3.alignment.aaindex.TestAAINDEXLoading Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 sec Running org.biojava3.alignment.SmithWatermanTest Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec Running org.biojava3.alignment.TestDNAAlignment Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.874 sec Running org.biojava3.alignment.SimpleAlignedSequenceTest Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 sec Results : Tests run: 215, Failures: 0, Errors: 0, Skipped: 3 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-alignment/target/biojava3-alignment-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT.jar 154K uploaded (biojava3-alignment-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-alignment' [INFO] Uploading project information for biojava3-alignment 3.0.4-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-alignment:3.0.4-SNAPSHOT' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT-sources.jar 138K uploaded (biojava3-alignment-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-alignment/3.0.4-SNAPSHOT/biojava3-alignment-3.0.4-SNAPSHOT-javadoc.jar 686K uploaded (biojava3-alignment-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-structure [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-structure/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 60 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 251 source files to /opt/cruise/projects/biojava-svn/biojava3-structure/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 30 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 43 source files to /opt/cruise/projects/biojava-svn/biojava3-structure/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-structure/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.structure.StructureTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.641 sec Running org.biojava.bio.structure.PDBStatusTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 sec Running org.biojava.bio.structure.StructurePairAlignerTest 1TAP is a LEGACY entry - this will most likely not parse correctly. Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.808 sec Running org.biojava.bio.structure.StructureToolsTest downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb7036651695335361089.gz copying to /tmp/hh/pdb4hhb.ent.gz Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.351 sec Running org.biojava.bio.structure.HeaderOnlyTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.624 sec Running org.biojava.bio.structure.io.TestChemCompProvider Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 sec Running org.biojava.bio.structure.PdbFileFormat30Test 104D is a LEGACY entry - this will most likely not parse correctly. Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.326 sec Running org.biojava.bio.structure.ElementTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.structure.SourceCompoundTest SOURCE INFO: Fragment? UNP RESIDUES 32-576 Organism Scientific: MUS MUSCULUS Organism Tax Id: 10090 Organism Common: MOUSE Gene: ACHE Expression System: HOMO SAPIENS Expression System Tax Id: 9606 Expression System Strain: HEK293F Expression System Vector Type: PLASMID Expression System Plasmid: PCDNA3.1 Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec Running org.biojava.bio.structure.align.util.AlignmentToolsTest Len1 Len2 AlignT OrderT Order 430 78 1.776000 0.001000 2 Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.79 sec Running org.biojava.bio.structure.TestDNAAlignment Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 sec Running org.biojava.bio.structure.scop.ScopTest Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation parsed 110800 scop sunid domains. parsed 143428 scop sunid descriptions. Setting ScopDatabase to type: org.biojava.bio.structure.scop.RemoteScopInstallation Setting ScopDatabase to type: org.biojava.bio.structure.scop.RemoteScopInstallation http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=4HHB http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=4hhb http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=1m02 http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=1CDG http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=81282 http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=1xzp http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=116879 http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=2bq6 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d2bq6a1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=57197 Setting ScopDatabase to type: org.biojava.bio.structure.scop.RemoteScopInstallation Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.244 sec Running org.biojava.bio.structure.ResidueNumberTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices Not testing shift vectors for blocks > 1. There is still a problem... Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.176 sec Running org.biojava.bio.structure.align.fatcat.FlipAFPChainTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.114 sec Running org.biojava.bio.structure.TestLoadStructureFromURL file:/tmp/SUB%20DIR/zn/pdb1znf.ent.gz fetching structure from URL:file:/tmp/SUB%20DIR/zn/pdb1znf.ent.gz?args=test structure 1ZNF models: 1 Title: THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER DNA-BINDING DOMAIN Classification: ZINC FINGER DNA BINDING DOMAIN IdCode: 1ZNF Resolution: 99.0 Technique: SOLUTION NMR Description: subset of 1ZNF null Authors: M.S.LEE,G.P.GIPPERT,K.V.SOMAN,D.A.CASE,P.E.WRIGHT DepDate: Mon Sep 25 00:00:00 PDT 1989 ModDate: Tue Feb 24 00:00:00 PST 2009 model[0]: chains: chain 0: >A< 31ST ZINC FINGER FROM XFIN length SEQRES: 0 length ATOM: 28 aminos: 25 hetatms: 3 nucleotides: 0 DBRefs: 1 DBREF 1ZNF A 1 25 UNP P08045 XFIN_XENLA 1044 1068 Molecules: Compound: 1 31ST ZINC FINGER FROM XFIN Engineered: YES ChainId: A Chains: OrganismScientific: XENOPUS LAEVIS OrganismCommon: AFRICAN CLAWED FROG OrganismTaxId: 8355 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec Running org.biojava.bio.structure.align.ce.OptimalCECPMainTest http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1qdmA1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47866 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1qdmA1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47866 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1qdmA1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47866 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 |============================================================================| .............................................................................. 78 alignments took 5.7090 s (73.2 ms avg) http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.017 sec Running org.biojava.bio.structure.align.FlipAFPChainTest mismatch in line: 1 line1: <AFPChain name1="1vhr.A" name2="2ihb.A" method="jCE Circular Permutation" version="1.1" alnLength="225" blockNum="2" gapLen="97" optLength="128" totalLenIni="178" alignScore="376.17" chainRmsd="4.72" identity="0.1328" normAlignScore="0.00" probability="3.29e+00" similarity="0.2500" similarity1="72" similarity2="40" totalRmsdIni="5.17" totalRmsdOpt="4.72" ca1Length="178" ca2Length="317" afpNum="13" alignScoreUpdate="0.00" time="0 line2: <AFPChain name1="1vhr.A" name2="2ihb.A" method="jCE Circular Permutation" version="1.1" alnLength="225" blockNum="2" gapLen="97" optLength="128" totalLenIni="178" alignScore="376.17" chainRmsd="4.72" identity="0.1328" normAlignScore="0.00" probability="3.29e+00" similarity="0.2500" similarity1="72" similarity2="40" totalRmsdIni="5.17" totalRmsdOpt="4.72" ca1Length="178" ca2Length="317" afpNum="13" alignScoreUpdate="0.00" time="4 mismatch at position 432 c1: 0 4 mismatch in line: 1 line1: <AFPChain name1="4hhb.A" name2="4hhb.B" method="jCE" version="1.1" alnLength="147" blockNum="1" gapLen="8" optLength="139" totalLenIni="141" alignScore="366.29" chainRmsd="1.49" identity="0.4317" normAlignScore="0.00" probability="6.47e+00" similarity="0.6115" similarity1="99" similarity2="95" totalRmsdIni="1.54" totalRmsdOpt="1.49" ca1Length="141" ca2Length="146" afpNum="3" alignScoreUpdate="0.00" time="0 line2: <AFPChain name1="4hhb.A" name2="4hhb.B" method="jCE" version="1.1" alnLength="147" blockNum="1" gapLen="8" optLength="139" totalLenIni="141" alignScore="366.29" chainRmsd="1.49" identity="0.4317" normAlignScore="0.00" probability="6.47e+00" similarity="0.6115" similarity1="99" similarity2="95" totalRmsdIni="1.54" totalRmsdOpt="1.49" ca1Length="141" ca2Length="146" afpNum="3" alignScoreUpdate="0.00" time="1 mismatch at position 409 c1: 0 1 Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.047 sec Running org.biojava.bio.structure.TestNucleotides Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec Running org.biojava.bio.structure.TestSECalignment unknown char U Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.458 sec Running org.biojava.bio.structure.align.LoadOldXMLfileTest loading 1P80.D 2IUF.E AFPChainXMLParser: warning: pos1: 726 D:753 pos2: -1 E:1710 should never be -1. Probably parsing an. Ignore h1: 5 10 linePos: 5 >65:D < Ignore h1: 8 10 linePos: 8 >2:E < loading 1FEZ.A 1O08.A Ignore h1: 5 10 linePos: 5 >5:A < Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.443 sec Running org.biojava.bio.structure.Test1a4w Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 sec Running org.biojava.bio.structure.MMcifTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.02 sec Running org.biojava.bio.structure.TestDownloadChemCompProvider reading /tmp/SUB DIR/chemcomp/_CON.cif.gz Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.structure.align.TestAlignDBSearchPairs Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.structure.TestVeryLongFileName Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.structure.PDBFileParserTest Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec Running org.biojava.bio.structure.ChemCompTest reading /tmp/SUB DIR/chemcomp/MEA.cif.gz reading /tmp/SUB DIR/chemcomp/PRR.cif.gz Problem with chemical component: PRR Did not find one letter code! Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.structure.SiteTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.structure.align.fatcat.TestOutputStrings Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.301 sec Running org.biojava.bio.structure.Test4hhb Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 sec Running org.biojava.bio.structure.align.ce.TestWebStartClient Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.structure.io.StructureSequenceMatcherTest Note: the following 10 warnings about missing residues are expected. Warning: chain E residue 38 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 39 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 40 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 41 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 42 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 43 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 44 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 45 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 46 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 47 in the Structure 2PTC has no corresponding amino acid in the sequence. Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec Running org.biojava.bio.structure.align.ce.CeCPMainTest creating new cache /tmp/remotepdpdomaindefs.ser http://source.rcsb.org/jfatcatserver/domains/getRepresentativePDPDomains got 22296 domain ranges for PDP domains from server. http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1wy5a2 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=82830 Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.836 sec Running org.biojava.bio.structure.scop.ScopDescriptionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.structure.HetatomImplTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec Running org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.192 sec Running org.biojava.bio.structure.TestAltLocs Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec Running org.biojava.bio.structure.align.ce.TestSmallAlignment Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec Running org.biojava.bio.structure.TestAtomCache Deleting /tmp//cm/pdb1cmw.ent.gz Deleting /tmp//hh/pdb1hhb.ent.gz Deleting /tmp//hh/pdb4hhb.ent.gz downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb5724389057895442131.gz copying to /tmp/hh/pdb4hhb.ent.gz Deleting /tmp//hh/pdb4hhb.ent.gz Problem while downloading PDB ID 1cmw from FTP server. java.io.FileNotFoundException: pub/pdb/data/structures/divided/pdb/cm/pdb1cmw.ent.gz at sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(FtpURLConnection.java:485) at java.net.URL.openStream(URL.java:1035) at org.biojava.bio.structure.io.util.FileDownloadUtils.downloadGzipCompressedFile(FileDownloadUtils.java:96) at org.biojava.bio.structure.io.PDBFileReader.downloadPDB(PDBFileReader.java:679) at org.biojava.bio.structure.io.PDBFileReader.downloadAndGetInputStream(PDBFileReader.java:796) at org.biojava.bio.structure.io.PDBFileReader.getInputStream(PDBFileReader.java:431) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:845) at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:569) at org.biojava.bio.structure.TestAtomCache.testFetchCurrent(TestAtomCache.java:169) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) problem loading:1CMW org.biojava.bio.structure.StructureException: could not find PDB 1cmw in file system and also could not download while parsing 1CMW at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:573) at org.biojava.bio.structure.TestAtomCache.testFetchCurrent(TestAtomCache.java:169) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Caused by: java.io.IOException: could not find PDB 1cmw in file system and also could not download at org.biojava.bio.structure.io.PDBFileReader.downloadAndGetInputStream(PDBFileReader.java:803) at org.biojava.bio.structure.io.PDBFileReader.getInputStream(PDBFileReader.java:431) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:845) at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:569) ... 24 more Please ignore previous exceptions. They are expected. downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb1367510700574545762.gz copying to /tmp/hh/pdb4hhb.ent.gz Deleting /tmp//hh/pdb4hhb.ent.gz downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/pdb/cm/pdb1cmw.ent.gz to /tmp/pdb1cmw4096861596013638940.gz copying to /tmp/cm/pdb1cmw.ent.gz downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/pdb/hh/pdb1hhb.ent.gz to /tmp/pdb1hhb5673240825030658872.gz copying to /tmp/hh/pdb1hhb.ent.gz Please ignore the previous four errors. They are expected for this ancient PDB. Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.894 sec Results : Tests run: 128, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] 55 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:64: warning - Tag @link: can't find getReplacement(String, boolean) in org.biojava.bio.structure.PDBStatus [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:218: warning - Tag @link: can't find getReplacement(String,boolean) in org.biojava.bio.structure.PDBStatus [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:103: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:103: warning - @param argument "statusStrUpper" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueNumber.java:84: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Structure.java:606: warning - @param argument "PDBCrystallographicInfo" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/StructureImpl.java:739: warning - @param argument "PDBCrystallographicInfo" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopDescription.java:166: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopDescription.java:144: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileConvert.java:320: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:46: warning - @link# is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:46: warning - @link# is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:248: warning - @returns is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:274: warning - @param argument "accepted" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureProvider.java:20: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureProvider.java:27: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:373: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:384: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:942: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:955: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:955: warning - @param argument "fetchCurrent" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/SandboxStyleStructureProvider.java:92: warning - @ is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:50: warning - Tag @see:illegal character: "123" in "{@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [WARNING] does the heavy lifting." [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:50: warning - Tag @see:illegal character: "64" in "{@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [WARNING] does the heavy lifting." [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:166: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:50: warning - Tag @see: reference not found: {@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [WARNING] does the heavy lifting. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java:430: warning - @param argument "flag" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/util/FileDownloadUtils.java:232: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeParameters.java:346: warning - @param argument "maxNrIterationsForOptimization" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:470: warning - Tag @link: can't find alignHeuristic(Atom[], Atom[], Object) in org.biojava.bio.structure.align.ce.OptimalCECPMain [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:190: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:48: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:48: warning - Parameter "name1" is documented more than once. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1039: warning - Tag @see: malformed: "#getOptLength(), the number of aligned residues in the final alignment." [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1361: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1039: warning - Tag @see: reference not found: #getOptLength(), the number of aligned residues in the final alignment. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AfpChainWriter.java:129: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AFPAlignmentDisplay.java:441: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:355: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:161: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:319: warning - @param argument "afpChain" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:393: warning - @param argument "<V>" is not a type parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:232: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:245: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:245: warning - @param argument "fetchCurrent" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:848: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/CacheFactory.java:12: warning - @Deprecated is an unknown tag -- same as a known tag except for case. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 60 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 30 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-structure/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.structure.StructureTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.645 sec Running org.biojava.bio.structure.PDBStatusTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec Running org.biojava.bio.structure.StructurePairAlignerTest 1TAP is a LEGACY entry - this will most likely not parse correctly. Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.816 sec Running org.biojava.bio.structure.StructureToolsTest downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb7624390303266921167.gz copying to /tmp/hh/pdb4hhb.ent.gz Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.247 sec Running org.biojava.bio.structure.HeaderOnlyTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.74 sec Running org.biojava.bio.structure.io.TestChemCompProvider Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec Running org.biojava.bio.structure.PdbFileFormat30Test 104D is a LEGACY entry - this will most likely not parse correctly. Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.36 sec Running org.biojava.bio.structure.ElementTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.structure.SourceCompoundTest SOURCE INFO: Fragment? UNP RESIDUES 32-576 Organism Scientific: MUS MUSCULUS Organism Tax Id: 10090 Organism Common: MOUSE Gene: ACHE Expression System: HOMO SAPIENS Expression System Tax Id: 9606 Expression System Strain: HEK293F Expression System Vector Type: PLASMID Expression System Plasmid: PCDNA3.1 Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 sec Running org.biojava.bio.structure.align.util.AlignmentToolsTest Len1 Len2 AlignT OrderT Order 430 78 1.768000 0.001000 2 Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.841 sec Running org.biojava.bio.structure.TestDNAAlignment Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 sec Running org.biojava.bio.structure.scop.ScopTest Setting ScopDatabase to type: org.biojava.bio.structure.scop.RemoteScopInstallation http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=4HHB http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=4hhb http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=1m02 http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=1CDG http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=81282 http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=1xzp http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=116879 http://source.rcsb.org/jfatcatserver/domains/getDomainsForPDB?pdbId=2bq6 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d2bq6a1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=57197 Setting ScopDatabase to type: org.biojava.bio.structure.scop.RemoteScopInstallation Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation parsed 110800 scop sunid domains. parsed 143428 scop sunid descriptions. Setting ScopDatabase to type: org.biojava.bio.structure.scop.RemoteScopInstallation Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.249 sec Running org.biojava.bio.structure.ResidueNumberTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices Not testing shift vectors for blocks > 1. There is still a problem... Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.611 sec Running org.biojava.bio.structure.align.fatcat.FlipAFPChainTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.081 sec Running org.biojava.bio.structure.TestLoadStructureFromURL file:/tmp/SUB%20DIR/zn/pdb1znf.ent.gz fetching structure from URL:file:/tmp/SUB%20DIR/zn/pdb1znf.ent.gz?args=test structure 1ZNF models: 1 Title: THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER DNA-BINDING DOMAIN Classification: ZINC FINGER DNA BINDING DOMAIN IdCode: 1ZNF Resolution: 99.0 Technique: SOLUTION NMR Description: subset of 1ZNF null Authors: M.S.LEE,G.P.GIPPERT,K.V.SOMAN,D.A.CASE,P.E.WRIGHT DepDate: Mon Sep 25 00:00:00 PDT 1989 ModDate: Tue Feb 24 00:00:00 PST 2009 model[0]: chains: chain 0: >A< 31ST ZINC FINGER FROM XFIN length SEQRES: 0 length ATOM: 28 aminos: 25 hetatms: 3 nucleotides: 0 DBRefs: 1 DBREF 1ZNF A 1 25 UNP P08045 XFIN_XENLA 1044 1068 Molecules: Compound: 1 31ST ZINC FINGER FROM XFIN ChainId: A Chains: Engineered: YES OrganismScientific: XENOPUS LAEVIS OrganismCommon: AFRICAN CLAWED FROG OrganismTaxId: 8355 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 sec Running org.biojava.bio.structure.align.ce.OptimalCECPMainTest http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1qdmA1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47866 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1qdmA1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47866 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1qdmA1 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47866 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 |============================================================================| .............................................................................. 78 alignments took 5.7240 s (73.4 ms avg) http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1nklA_ http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=47863 Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.021 sec Running org.biojava.bio.structure.align.FlipAFPChainTest mismatch in line: 1 line1: <AFPChain name1="1vhr.A" name2="2ihb.A" method="jCE Circular Permutation" version="1.1" alnLength="225" blockNum="2" gapLen="97" optLength="128" totalLenIni="178" alignScore="376.17" chainRmsd="4.72" identity="0.1328" normAlignScore="0.00" probability="3.29e+00" similarity="0.2500" similarity1="72" similarity2="40" totalRmsdIni="5.17" totalRmsdOpt="4.72" ca1Length="178" ca2Length="317" afpNum="13" alignScoreUpdate="0.00" time="0 line2: <AFPChain name1="1vhr.A" name2="2ihb.A" method="jCE Circular Permutation" version="1.1" alnLength="225" blockNum="2" gapLen="97" optLength="128" totalLenIni="178" alignScore="376.17" chainRmsd="4.72" identity="0.1328" normAlignScore="0.00" probability="3.29e+00" similarity="0.2500" similarity1="72" similarity2="40" totalRmsdIni="5.17" totalRmsdOpt="4.72" ca1Length="178" ca2Length="317" afpNum="13" alignScoreUpdate="0.00" time="4 mismatch at position 432 c1: 0 4 mismatch in line: 1 line1: <AFPChain name1="4hhb.A" name2="4hhb.B" method="jCE" version="1.1" alnLength="147" blockNum="1" gapLen="8" optLength="139" totalLenIni="141" alignScore="366.29" chainRmsd="1.49" identity="0.4317" normAlignScore="0.00" probability="6.47e+00" similarity="0.6115" similarity1="99" similarity2="95" totalRmsdIni="1.54" totalRmsdOpt="1.49" ca1Length="141" ca2Length="146" afpNum="3" alignScoreUpdate="0.00" time="0 line2: <AFPChain name1="4hhb.A" name2="4hhb.B" method="jCE" version="1.1" alnLength="147" blockNum="1" gapLen="8" optLength="139" totalLenIni="141" alignScore="366.29" chainRmsd="1.49" identity="0.4317" normAlignScore="0.00" probability="6.47e+00" similarity="0.6115" similarity1="99" similarity2="95" totalRmsdIni="1.54" totalRmsdOpt="1.49" ca1Length="141" ca2Length="146" afpNum="3" alignScoreUpdate="0.00" time="1 mismatch at position 409 c1: 0 1 Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.044 sec Running org.biojava.bio.structure.TestNucleotides Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec Running org.biojava.bio.structure.TestSECalignment unknown char U Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.352 sec Running org.biojava.bio.structure.align.LoadOldXMLfileTest loading 1P80.D 2IUF.E AFPChainXMLParser: warning: pos1: 726 D:753 pos2: -1 E:1710 should never be -1. Probably parsing an. Ignore h1: 5 10 linePos: 5 >65:D < Ignore h1: 8 10 linePos: 8 >2:E < loading 1FEZ.A 1O08.A Ignore h1: 5 10 linePos: 5 >5:A < Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 sec Running org.biojava.bio.structure.Test1a4w Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 sec Running org.biojava.bio.structure.MMcifTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.251 sec Running org.biojava.bio.structure.TestDownloadChemCompProvider reading /tmp/SUB DIR/chemcomp/_CON.cif.gz Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.structure.align.TestAlignDBSearchPairs Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec Running org.biojava.bio.structure.TestVeryLongFileName Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec Running org.biojava.bio.structure.PDBFileParserTest Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec Running org.biojava.bio.structure.ChemCompTest reading /tmp/SUB DIR/chemcomp/MEA.cif.gz reading /tmp/SUB DIR/chemcomp/PRR.cif.gz Problem with chemical component: PRR Did not find one letter code! Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.structure.SiteTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.structure.align.fatcat.TestOutputStrings Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.288 sec Running org.biojava.bio.structure.Test4hhb Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.499 sec Running org.biojava.bio.structure.align.ce.TestWebStartClient Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.structure.io.StructureSequenceMatcherTest Note: the following 10 warnings about missing residues are expected. Warning: chain E residue 38 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 39 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 40 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 41 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 42 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 43 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 44 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 45 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 46 in the Structure 2PTC has no corresponding amino acid in the sequence. Warning: chain E residue 47 in the Structure 2PTC has no corresponding amino acid in the sequence. Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 sec Running org.biojava.bio.structure.align.ce.CeCPMainTest creating new cache /tmp/remotepdpdomaindefs.ser http://source.rcsb.org/jfatcatserver/domains/getRepresentativePDPDomains got 22296 domain ranges for PDP domains from server. http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1wy5a2 http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=82830 Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.916 sec Running org.biojava.bio.structure.scop.ScopDescriptionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.structure.HetatomImplTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 sec Running org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.41 sec Running org.biojava.bio.structure.TestAltLocs Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec Running org.biojava.bio.structure.align.ce.TestSmallAlignment Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec Running org.biojava.bio.structure.TestAtomCache Deleting /tmp//cm/pdb1cmw.ent.gz Deleting /tmp//hh/pdb1hhb.ent.gz Deleting /tmp//hh/pdb4hhb.ent.gz downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb428443217736342351.gz copying to /tmp/hh/pdb4hhb.ent.gz Deleting /tmp//hh/pdb4hhb.ent.gz Problem while downloading PDB ID 1cmw from FTP server. java.io.FileNotFoundException: pub/pdb/data/structures/divided/pdb/cm/pdb1cmw.ent.gz at sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(FtpURLConnection.java:485) at java.net.URL.openStream(URL.java:1035) at org.biojava.bio.structure.io.util.FileDownloadUtils.downloadGzipCompressedFile(FileDownloadUtils.java:96) at org.biojava.bio.structure.io.PDBFileReader.downloadPDB(PDBFileReader.java:679) at org.biojava.bio.structure.io.PDBFileReader.downloadAndGetInputStream(PDBFileReader.java:796) at org.biojava.bio.structure.io.PDBFileReader.getInputStream(PDBFileReader.java:431) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:845) at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:569) at org.biojava.bio.structure.TestAtomCache.testFetchCurrent(TestAtomCache.java:169) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) problem loading:1CMW org.biojava.bio.structure.StructureException: could not find PDB 1cmw in file system and also could not download while parsing 1CMW at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:573) at org.biojava.bio.structure.TestAtomCache.testFetchCurrent(TestAtomCache.java:169) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Caused by: java.io.IOException: could not find PDB 1cmw in file system and also could not download at org.biojava.bio.structure.io.PDBFileReader.downloadAndGetInputStream(PDBFileReader.java:803) at org.biojava.bio.structure.io.PDBFileReader.getInputStream(PDBFileReader.java:431) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:845) at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:569) ... 24 more Please ignore previous exceptions. They are expected. downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb7067597505849958324.gz copying to /tmp/hh/pdb4hhb.ent.gz Deleting /tmp//hh/pdb4hhb.ent.gz downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/pdb/cm/pdb1cmw.ent.gz to /tmp/pdb1cmw6181194383104687232.gz copying to /tmp/cm/pdb1cmw.ent.gz downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/pdb/hh/pdb1hhb.ent.gz to /tmp/pdb1hhb177257535835448390.gz copying to /tmp/hh/pdb1hhb.ent.gz Please ignore the previous four errors. They are expected for this ancient PDB. Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.909 sec Results : Tests run: 128, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure/target/biojava3-structure-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT.jar 812K uploaded (biojava3-structure-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-structure:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-structure' [INFO] Uploading project information for biojava3-structure 3.0.4-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT-sources.jar 679K uploaded (biojava3-structure-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure/3.0.4-SNAPSHOT/biojava3-structure-3.0.4-SNAPSHOT-javadoc.jar 2893K uploaded (biojava3-structure-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-structure-gui [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 14 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 100 source files to /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 6 source files to /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.structure.gui.ViewerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec Running org.biojava.structure.gui.RenderStyleTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.structure.gui.StructureViewerTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec Running org.biojava.bio.structure.gui.TestAtomInfo Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec Running org.biojava.structure.gui.JmolViewerImplTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Results : Tests run: 14, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://logging.apache.org/log4j/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/regexp/apidocs/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/velocity/api/package-list. Ignored it. [INFO] 19 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ContinuousColorMapperTransform.java:65: warning - @param argument "the" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/DefaultMatrixMapper.java:49: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:186: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:194: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:201: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:145: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:88: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:223: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:233: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:254: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:271: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:108: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:120: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:86: warning - @param argument "type" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:86: warning - @param argument "numcomponents" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/LinearColorInterpolator.java:147: warning - @param argument "interpDirection" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java:143: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DotPlotPanel.java:67: warning - @param argument "background" is not a parameter name. [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 14 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 1 source file to /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.structure.gui.ViewerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 sec Running org.biojava.structure.gui.RenderStyleTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.structure.gui.StructureViewerTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec Running org.biojava.bio.structure.gui.TestAtomInfo Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec Running org.biojava.structure.gui.JmolViewerImplTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Results : Tests run: 14, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-structure-gui/target/biojava3-structure-gui-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT.jar 292K uploaded (biojava3-structure-gui-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-structure-gui' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-structure-gui:3.0.4-SNAPSHOT' [INFO] Uploading project information for biojava3-structure-gui 3.0.4-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT-sources.jar 186K uploaded (biojava3-structure-gui-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-structure-gui/3.0.4-SNAPSHOT/biojava3-structure-gui-3.0.4-SNAPSHOT-javadoc.jar 1064K uploaded (biojava3-structure-gui-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-genome [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-genome/target [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/testoutput (includes = [**/volvox_all.faa], excludes = []) |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 20 source files to /opt/cruise/projects/biojava-svn/biojava3-genome/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 10 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 2 source files to /opt/cruise/projects/biojava-svn/biojava3-genome/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-genome/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.genome.GeneFeatureHelperTest May 15, 2012 2:01:29 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3 May 15, 2012 2:01:29 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3 May 15, 2012 2:01:29 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading src/test/resources/amphimedon.gff3 Gene EDEN found at ctgA 1050 9000 POSITIVE Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE May 15, 2012 2:01:29 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3 Note [protein kinase] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.649 sec Running org.biojava3.genome.AppTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Results : Tests run: 7, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://logging.apache.org/log4j/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/regexp/apidocs/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/velocity/api/package-list. Ignored it. [INFO] 6 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:181: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:331: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureHelper.java:24: warning - @return tag has no arguments. [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. [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. [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-genome/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.genome.GeneFeatureHelperTest May 15, 2012 2:01:34 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading src/test/resources/amphimedon.gff3 Gene EDEN found at ctgA 1050 9000 POSITIVE Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE May 15, 2012 2:01:34 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3 Note [protein kinase] May 15, 2012 2:01:34 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3 May 15, 2012 2:01:34 PM org.biojava3.genome.parsers.gff.GFF3Reader read INFO: Gff.read(): Reading /opt/cruise/projects/biojava-svn/biojava3-genome/src/test/resources/volvox.gff3 Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.676 sec Running org.biojava3.genome.AppTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Results : Tests run: 7, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-genome/target/biojava3-genome-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT.jar 59K uploaded (biojava3-genome-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-genome' [INFO] Uploading project information for biojava3-genome 3.0.4-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-genome:3.0.4-SNAPSHOT' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT-sources.jar 40K uploaded (biojava3-genome-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-genome/3.0.4-SNAPSHOT/biojava3-genome-3.0.4-SNAPSHOT-javadoc.jar 261K uploaded (biojava3-genome-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-modfinder [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-modfinder/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 21 source files to /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 4 source files to /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.protmod.structure.ProteinModificationRegistryTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 sec Running org.biojava3.protmod.structure.ProteinModificationParserTest reading /tmp/chemcomp/PRO.cif.gz reading /tmp/chemcomp/SER.cif.gz reading /tmp/chemcomp/ALA.cif.gz reading /tmp/chemcomp/LEU.cif.gz reading /tmp/chemcomp/THR.cif.gz reading /tmp/chemcomp/GLN.cif.gz reading /tmp/chemcomp/GLY.cif.gz reading /tmp/chemcomp/VAL.cif.gz reading /tmp/chemcomp/ILE.cif.gz reading /tmp/chemcomp/CYS.cif.gz reading /tmp/chemcomp/ASP.cif.gz reading /tmp/chemcomp/TYR.cif.gz reading /tmp/chemcomp/ASN.cif.gz reading /tmp/chemcomp/TRP.cif.gz reading /tmp/chemcomp/HIS.cif.gz reading /tmp/chemcomp/LYS.cif.gz reading /tmp/chemcomp/GLU.cif.gz reading /tmp/chemcomp/ARG.cif.gz reading /tmp/chemcomp/PHE.cif.gz reading /tmp/chemcomp/ACE.cif.gz reading /tmp/chemcomp/DPN.cif.gz reading /tmp/chemcomp/DPR.cif.gz reading /tmp/chemcomp/NH2.cif.gz Did not identify any modified compounds for 1MCC reading /tmp/chemcomp/MET.cif.gz Did not identify any modified compounds for 1SCY reading /tmp/chemcomp/NRQ.cif.gz reading /tmp/chemcomp/CA.cif.gz reading /tmp/chemcomp/ACY.cif.gz reading /tmp/chemcomp/HOH.cif.gz Did not identify any modified compounds for 1UIS reading /tmp/chemcomp/TPO.cif.gz reading /tmp/chemcomp/SEP.cif.gz reading /tmp/chemcomp/XFE.cif.gz Did not identify any modified compounds for 3MVJ reading /tmp/chemcomp/TYS.cif.gz reading /tmp/chemcomp/1Z0.cif.gz reading /tmp/chemcomp/NAG.cif.gz reading /tmp/chemcomp/NA.cif.gz Did not identify any modified compounds for 1DOJ Did not identify any modified compounds for 1UIS reading /tmp/chemcomp/MAN.cif.gz Did not identify any modified compounds for 3M6S reading /tmp/chemcomp/SF4.cif.gz reading /tmp/chemcomp/F3S.cif.gz Did not identify any modified compounds for 1A6L reading /tmp/chemcomp/FES.cif.gz Did not identify any modified compounds for 1A70 Did not identify any modified compounds for 1RPB reading /tmp/chemcomp/HCA.cif.gz reading /tmp/chemcomp/CFM.cif.gz reading /tmp/chemcomp/CLP.cif.gz Did not identify any modified compounds for 1FP4 reading /tmp/chemcomp/MSE.cif.gz reading /tmp/chemcomp/CRO.cif.gz Did not identify any modified compounds for 1EMA reading /tmp/chemcomp/CU.cif.gz reading /tmp/chemcomp/CUZ.cif.gz reading /tmp/chemcomp/IOD.cif.gz reading /tmp/chemcomp/CL.cif.gz Did not identify any modified compounds for 2IWK reading /tmp/chemcomp/NFS.cif.gz Did not identify any modified compounds for 1SU6 reading /tmp/chemcomp/ZN.cif.gz reading /tmp/chemcomp/FAD.cif.gz reading /tmp/chemcomp/ABL.cif.gz Did not identify any modified compounds for 2AXR reading /tmp/chemcomp/S3H.cif.gz reading /tmp/chemcomp/PO4.cif.gz Did not identify any modified compounds for 3H8L reading /tmp/chemcomp/FE.cif.gz Did not identify any modified compounds for 1CAD Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.229 sec Running org.biojava3.protmod.structure.ModifiedCompoundSerializationTest reading /tmp/chemcomp/MAL.cif.gz reading /tmp/chemcomp/FMN.cif.gz reading /tmp/chemcomp/ADP.cif.gz reading /tmp/chemcomp/QWE.cif.gz Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.554 sec Results : Tests run: 11, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://logging.apache.org/log4j/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/regexp/apidocs/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/velocity/api/package-list. Ignored it. [INFO] 19 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java:43: warning - Tag @link: reference not found: register [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java:43: warning - Tag @link: reference not found: of [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java:122: warning - @param argument "pdbccIds" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ProteinModificationRegistry.java:212: warning - @param argument "mod" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:79: warning - Tag @see: can't find getLinkedGroupPairs in org.biojava3.protmod.structure.ModifiedCompound [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:85: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:52: warning - Tag @link: reference not found: ProteinModificationBean [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:85: warning - @return tag cannot be used in method with void return type. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:93: warning - Tag @link: reference not found: addGroup [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompoundImpl.java:77: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:52: warning - Tag @link: reference not found: ProteinModificationBean [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:93: warning - Tag @link: reference not found: addGroup [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ProteinModificationIdentifier.java:123: warning - @param argument "recordUnidentifiableAtomLinkages" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/StructureUtil.java:282: warning - @return tag has no arguments. [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.protmod.structure.ProteinModificationRegistryTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.572 sec Running org.biojava3.protmod.structure.ProteinModificationParserTest reading /tmp/chemcomp/PRO.cif.gz reading /tmp/chemcomp/SER.cif.gz reading /tmp/chemcomp/ALA.cif.gz reading /tmp/chemcomp/LEU.cif.gz reading /tmp/chemcomp/THR.cif.gz reading /tmp/chemcomp/GLN.cif.gz reading /tmp/chemcomp/GLY.cif.gz reading /tmp/chemcomp/VAL.cif.gz reading /tmp/chemcomp/ILE.cif.gz reading /tmp/chemcomp/CYS.cif.gz reading /tmp/chemcomp/ASP.cif.gz reading /tmp/chemcomp/TYR.cif.gz reading /tmp/chemcomp/ASN.cif.gz reading /tmp/chemcomp/TRP.cif.gz reading /tmp/chemcomp/HIS.cif.gz reading /tmp/chemcomp/LYS.cif.gz reading /tmp/chemcomp/GLU.cif.gz reading /tmp/chemcomp/ARG.cif.gz reading /tmp/chemcomp/PHE.cif.gz reading /tmp/chemcomp/ACE.cif.gz reading /tmp/chemcomp/DPN.cif.gz reading /tmp/chemcomp/DPR.cif.gz reading /tmp/chemcomp/NH2.cif.gz Did not identify any modified compounds for 1MCC reading /tmp/chemcomp/MET.cif.gz Did not identify any modified compounds for 1SCY reading /tmp/chemcomp/NRQ.cif.gz reading /tmp/chemcomp/CA.cif.gz reading /tmp/chemcomp/ACY.cif.gz reading /tmp/chemcomp/HOH.cif.gz Did not identify any modified compounds for 1UIS reading /tmp/chemcomp/TPO.cif.gz reading /tmp/chemcomp/SEP.cif.gz reading /tmp/chemcomp/XFE.cif.gz Did not identify any modified compounds for 3MVJ reading /tmp/chemcomp/TYS.cif.gz reading /tmp/chemcomp/1Z0.cif.gz reading /tmp/chemcomp/NAG.cif.gz reading /tmp/chemcomp/NA.cif.gz Did not identify any modified compounds for 1DOJ Did not identify any modified compounds for 1UIS reading /tmp/chemcomp/MAN.cif.gz Did not identify any modified compounds for 3M6S reading /tmp/chemcomp/SF4.cif.gz reading /tmp/chemcomp/F3S.cif.gz Did not identify any modified compounds for 1A6L reading /tmp/chemcomp/FES.cif.gz Did not identify any modified compounds for 1A70 Did not identify any modified compounds for 1RPB reading /tmp/chemcomp/HCA.cif.gz reading /tmp/chemcomp/CFM.cif.gz reading /tmp/chemcomp/CLP.cif.gz Did not identify any modified compounds for 1FP4 reading /tmp/chemcomp/MSE.cif.gz reading /tmp/chemcomp/CRO.cif.gz Did not identify any modified compounds for 1EMA reading /tmp/chemcomp/CU.cif.gz reading /tmp/chemcomp/CUZ.cif.gz reading /tmp/chemcomp/IOD.cif.gz reading /tmp/chemcomp/CL.cif.gz Did not identify any modified compounds for 2IWK reading /tmp/chemcomp/NFS.cif.gz Did not identify any modified compounds for 1SU6 reading /tmp/chemcomp/ZN.cif.gz reading /tmp/chemcomp/FAD.cif.gz reading /tmp/chemcomp/ABL.cif.gz Did not identify any modified compounds for 2AXR reading /tmp/chemcomp/S3H.cif.gz reading /tmp/chemcomp/PO4.cif.gz Did not identify any modified compounds for 3H8L reading /tmp/chemcomp/FE.cif.gz Did not identify any modified compounds for 1CAD Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.221 sec Running org.biojava3.protmod.structure.ModifiedCompoundSerializationTest reading /tmp/chemcomp/FMN.cif.gz reading /tmp/chemcomp/ADP.cif.gz reading /tmp/chemcomp/QWE.cif.gz reading /tmp/chemcomp/MAL.cif.gz Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.565 sec Results : Tests run: 11, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-modfinder/target/biojava3-modfinder-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT.jar 88K uploaded (biojava3-modfinder-3.0.4-SNAPSHOT.jar) [INFO] Uploading project information for biojava3-modfinder 3.0.4-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-modfinder:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-modfinder' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT-sources.jar 68K uploaded (biojava3-modfinder-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-modfinder/3.0.4-SNAPSHOT/biojava3-modfinder-3.0.4-SNAPSHOT-javadoc.jar 255K uploaded (biojava3-modfinder-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-ws [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-ws/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 20 source files to /opt/cruise/projects/biojava-svn/biojava3-ws/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-ws/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- There are no tests to run. Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://logging.apache.org/log4j/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/regexp/apidocs/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/velocity/api/package-list. Ignored it. [INFO] 11 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:52: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastJob.java:40: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:154: warning - Tag @link: can't find printRemoteBlastInfo() in org.biojava3.ws.alignment.qblast.NCBIQBlastService [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:154: warning - @param argument "db" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:177: warning - @param argument "expect:" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:225: warning - @param argument "word:" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:377: warning - #DEFAULT_TOOL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:386: warning - #DEFAULT_TOOL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:395: warning - #DEFAULT_EMAIL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:404: warning - #DEFAULT_EMAIL (referenced by @value tag) is an unknown reference. [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-ws/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- There are no tests to run. Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-ws/target/biojava3-ws-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT.jar 35K uploaded (biojava3-ws-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-ws:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-ws' [INFO] Uploading project information for biojava3-ws 3.0.4-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT-sources.jar 28K uploaded (biojava3-ws-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-ws/3.0.4-SNAPSHOT/biojava3-ws-3.0.4-SNAPSHOT-javadoc.jar 221K uploaded (biojava3-ws-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-protein-disorder [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 10 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 12 source files to /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 2 source files to /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.ronn.JronnTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.345 sec Results : Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://logging.apache.org/log4j/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/regexp/apidocs/package-list. Ignored it. [ERROR] Error fetching link: http://jakarta.apache.org/velocity/api/package-list. Ignored it. [INFO] 3 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java:220: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java:237: warning - Tag @see: can't find Jronn.Range in org.biojava3.ronn.Jronn [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 10 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 2 source files to /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava3.ronn.JronnTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.376 sec Results : Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT.jar
to /home/andreas/.m2/repository/org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/target/biojava3-protein-disorder-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT.jar 242K uploaded (biojava3-protein-disorder-3.0.4-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-protein-disorder' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-protein-disorder:3.0.4-SNAPSHOT' [INFO] Uploading project information for biojava3-protein-disorder 3.0.4-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT-sources.jar 233K uploaded (biojava3-protein-disorder-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-protein-disorder/3.0.4-SNAPSHOT/biojava3-protein-disorder-3.0.4-SNAPSHOT-javadoc.jar 161K uploaded (biojava3-protein-disorder-3.0.4-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-aa-prop [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 10 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 31 source files to /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 8 source files to /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- There are no tests to run. Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT.jar |
| assembly:single {execution: make-assembly} |
| [INFO] Processing DependencySet (output=) [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/AAProperties-jar-with-dependencies.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/AAProperties-jar-with-dependencies.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] 3 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java:21: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java:21: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 10 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 4 source files to /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- There are no tests to run. Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| assembly:single {execution: make-assembly} |
| [INFO] Processing DependencySet (output=) [INFO] Building jar: /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/AAProperties-jar-with-dependencies.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/AAProperties-jar-with-dependencies.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/biojava3-aa-prop-3.0.4-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-javadoc.jar [INFO] Installing /opt/cruise/projects/biojava-svn/biojava3-aa-prop/target/AAProperties-jar-with-dependencies.jar to /home/andreas/.m2/repository/org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT.jar 72K uploaded (biojava3-aa-prop-3.0.4-SNAPSHOT.jar) [INFO] Uploading project information for biojava3-aa-prop 3.0.4-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava3-aa-prop:3.0.4-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava3-aa-prop' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar 2513K uploaded (biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-sources.jar 50K uploaded (biojava3-aa-prop-3.0.4-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-javadoc.jar 342K uploaded (biojava3-aa-prop-3.0.4-SNAPSHOT-javadoc.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava3-aa-prop/3.0.4-SNAPSHOT/biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar 2513K uploaded (biojava3-aa-prop-3.0.4-SNAPSHOT-jar-with-dependencies.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] task-segment: [javadoc:aggregate] (aggregator-style) [INFO] ------------------------------------------------------------------------ [INFO] Preparing javadoc:aggregate [INFO] ------------------------------------------------------------------------ [INFO] Building biojava [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-core [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-phylo [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-sequencing [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-alignment [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-structure [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-structure-gui [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-genome [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-modfinder [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-ws [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-protein-disorder [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [INFO] ------------------------------------------------------------------------ [INFO] Building biojava3-aa-prop [INFO] ------------------------------------------------------------------------ [INFO] No goals needed for project - skipping [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:aggregate {execution: default-cli} |
| [INFO] 297 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:36: warning - Tag @link: reference not found: http://www.sequenceontology.org/gff3.shtml [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "58" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://www.sequenceontology.org/gff3.shtml" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "58" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "126" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link:illegal character: "47" in "http://biowiki.org/~yam/bioe131/GFF.ppt" [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:564: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link: reference not found: http://www.sequenceontology.org/gff3.shtml [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java:87: warning - Tag @link: reference not found: http://biowiki.org/~yam/bioe131/GFF.ppt [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:132: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:144: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:105: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java:114: warning - @return tag has no arguments. [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. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:103: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:95: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:111: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:122: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java:85: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:600: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:104: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:92: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:190: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:134: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:204: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:213: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:77: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:231: warning - @param argument "startCodonSequence" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java:246: warning - @param argument "stopCodonSequence" is not a parameter name. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @ is an unknown tag. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:62: warning - @ is an unknown tag. [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:74: warning - @ is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java:74: warning - @ is an unknown tag. [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 [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:244: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:235: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:109: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:118: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:168: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:127: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:253: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:136: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:144: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:88: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:99: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:227: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java:152: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:146: warning - Tag @link: can't find countCompounds(org.biojava3.core.sequence.template.Sequence, C[]) in org.biojava3.core.sequence.template.SequenceMixin [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:96: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java:61: warning - @param argument "br" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:115: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:51: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:100: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:69: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java:85: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaWriterHelper.java:103: warning - @param argument "dnaSequences" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:96: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:86: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java:72: warning - @return tag has no arguments. [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. [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. [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. [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. [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. [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. [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. [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:287: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:278: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:220: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:150: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:256: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:162: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:296: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:174: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:141: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:196: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:207: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:234: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:245: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java:185: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:259: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:238: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:183: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:140: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:230: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:466: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:149: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:192: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:446: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:158: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:131: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:424: warning - @return tag has no arguments. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:203: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:214: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:222: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java:167: warning - @return tag has no arguments. [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. [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java:114: warning - @param argument "<C>" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java:125: warning - @param argument "<C>" is not a parameter name. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:591: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:529: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:538: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:348: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:331: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:311: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:404: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:520: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:574: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:171: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:582: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:144: warning - @param argument "bioBegin" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:162: warning - @param argument "bioEnd" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:194: warning - @param argument "annotation" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:331: warning - @param argument "featureType" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:469: warning - @param argument "species" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @param argument "begin" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java:511: warning - @param argument "end" is not a parameter name. [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 [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 [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. [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/util/StringManipulationHelper.java:73: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/util/StringManipulationHelper.java:73: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:64: warning - Tag @link: can't find getReplacement(String, boolean) in org.biojava.bio.structure.PDBStatus [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:218: warning - Tag @link: can't find getReplacement(String,boolean) in org.biojava.bio.structure.PDBStatus [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:103: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java:103: warning - @param argument "statusStrUpper" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueNumber.java:84: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Structure.java:606: warning - @param argument "PDBCrystallographicInfo" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/StructureImpl.java:739: warning - @param argument "PDBCrystallographicInfo" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopDescription.java:166: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopDescription.java:144: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileConvert.java:320: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:46: warning - @link# is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:46: warning - @link# is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:248: warning - @returns is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java:274: warning - @param argument "accepted" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureProvider.java:20: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureProvider.java:27: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:373: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:384: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:942: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:955: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java:955: warning - @param argument "fetchCurrent" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/SandboxStyleStructureProvider.java:92: warning - @ is an unknown tag. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:50: warning - Tag @see:illegal character: "123" in "{@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [WARNING] does the heavy lifting." [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:50: warning - Tag @see:illegal character: "64" in "{@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [WARNING] does the heavy lifting." [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:166: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java:50: warning - Tag @see: reference not found: {@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which [WARNING] does the heavy lifting. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider.java:430: warning - @param argument "flag" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/io/util/FileDownloadUtils.java:232: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeParameters.java:346: warning - @param argument "maxNrIterationsForOptimization" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:470: warning - Tag @link: can't find alignHeuristic(Atom[], Atom[], Object) in org.biojava.bio.structure.align.ce.OptimalCECPMain [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:190: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:48: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java:48: warning - Parameter "name1" is documented more than once. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1039: warning - Tag @see: malformed: "#getOptLength(), the number of aligned residues in the final alignment." [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1361: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java:1039: warning - Tag @see: reference not found: #getOptLength(), the number of aligned residues in the final alignment. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AfpChainWriter.java:129: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AFPAlignmentDisplay.java:441: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:355: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:161: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:319: warning - @param argument "afpChain" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java:393: warning - @param argument "<V>" is not a type parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:232: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:245: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:245: warning - @param argument "fetchCurrent" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java:848: warning - Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/CacheFactory.java:12: warning - @Deprecated is an unknown tag -- same as a known tag except for case. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ContinuousColorMapperTransform.java:65: warning - @param argument "the" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/DefaultMatrixMapper.java:49: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:186: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:194: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:201: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:145: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:88: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:223: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:233: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:254: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java:271: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:108: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:120: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:86: warning - @param argument "type" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java:86: warning - @param argument "numcomponents" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/LinearColorInterpolator.java:147: warning - @param argument "interpDirection" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java:143: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DotPlotPanel.java:67: warning - @param argument "background" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:181: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java:331: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureHelper.java:24: warning - @return tag has no arguments. [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. [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. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java:43: warning - Tag @link: reference not found: register [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java:43: warning - Tag @link: reference not found: of [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java:122: warning - @param argument "pdbccIds" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:63: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86: warning - @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java:86: warning - @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/ProteinModificationRegistry.java:212: warning - @param argument "mod" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:79: warning - Tag @see: can't find getLinkedGroupPairs in org.biojava3.protmod.structure.ModifiedCompound [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:85: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:52: warning - Tag @link: reference not found: ProteinModificationBean [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:85: warning - @return tag cannot be used in method with void return type. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:93: warning - Tag @link: reference not found: addGroup [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompoundImpl.java:77: warning - Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:52: warning - Tag @link: reference not found: ProteinModificationBean [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java:93: warning - Tag @link: reference not found: addGroup [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ProteinModificationIdentifier.java:123: warning - @param argument "recordUnidentifiableAtomLinkages" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/StructureUtil.java:282: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:52: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastJob.java:40: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:154: warning - Tag @link: can't find printRemoteBlastInfo() in org.biojava3.ws.alignment.qblast.NCBIQBlastService [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:154: warning - @param argument "db" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:177: warning - @param argument "expect:" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:225: warning - @param argument "word:" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:377: warning - #DEFAULT_TOOL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:386: warning - #DEFAULT_TOOL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:395: warning - #DEFAULT_EMAIL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java:404: warning - #DEFAULT_EMAIL (referenced by @value tag) is an unknown reference. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java:220: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java:237: warning - Tag @see: can't find Jronn.Range in org.biojava3.ronn.Jronn [WARNING] /opt/cruise/projects/biojava-svn/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java:21: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-svn/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java:21: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. [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 [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 [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 [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 [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [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 [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 [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java:154: warning - Tag @link: reference not found: SequenceMixin.SequenceIterator [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [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 [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 [WARNING] /opt/cruise/projects/biojava-svn/biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java:154: warning - Tag @link: reference not found: subtract [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] ------------------------------------------------------------------------ [INFO] biojava ............................................... SUCCESS [26.151s] [INFO] biojava3-core ......................................... SUCCESS [1:02.850s] [INFO] biojava3-phylo ........................................ SUCCESS [39.079s] [INFO] biojava3-sequencing ................................... SUCCESS [47.260s] [INFO] biojava3-alignment .................................... SUCCESS [56.294s] [INFO] biojava3-structure .................................... SUCCESS [3:17.149s] [INFO] biojava3-structure-gui ................................ SUCCESS [1:04.478s] [INFO] biojava3-genome ....................................... SUCCESS [48.114s] [INFO] biojava3-modfinder .................................... SUCCESS [52.156s] [INFO] biojava3-ws ........................................... SUCCESS [41.979s] [INFO] biojava3-protein-disorder ............................. SUCCESS [51.912s] [INFO] biojava3-aa-prop ...................................... SUCCESS [1:22.941s] [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESSFUL [INFO] ------------------------------------------------------------------------ [INFO] Total time: 13 minutes 19 seconds [INFO] Finished at: Tue May 15 14:06:30 PDT 2012 [INFO] Final Memory: 92M/2364M [INFO] ------------------------------------------------------------------------ |
| Unit Tests: (0) | |||
| No Tests Run | |||
| This project doesn't have any tests | |||
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