[ImageJ-builds] Build failed in Jenkins: Colocalisation_Analysis #12

[jenkins at imagej.net]

See <http://jenkins.imagej.net/job/Colocalisation_Analysis/12/changes>

Changes:

[Curtis Rueden] POM: tweak repositories comment

[Curtis Rueden] POM: bump to pom-fiji 5.0

[Curtis Rueden] POM: tidy up order of configuration blocks

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[...truncated 51 lines...]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ Colocalisation_Analysis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ Colocalisation_Analysis ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 12 source files to /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/test-classes
[WARNING] Note: /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/test/java/tests/TestImageAccessor.java uses or overrides a deprecated API.
[WARNING] Note: Recompile with -Xlint:deprecation for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ Colocalisation_Analysis ---
[INFO] Surefire report directory: /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running tests.KendallTauTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.041 sec - in tests.KendallTauTest
Running tests.StatisticsTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec - in tests.StatisticsTest
Running tests.MaskAndRoiTest
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.054 sec - in tests.MaskAndRoiTest
Running tests.MandersColocalizationTest
java.io.IOException: Stream closed
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec - in tests.MandersColocalizationTest
Running tests.PearsonsCorrelationTest
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.001 sec - in tests.PearsonsCorrelationTest
Running tests.SpearmanRankTest
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
java.io.IOException: Stream closed
Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.001 sec - in tests.SpearmanRankTest
Running tests.CostesSignificanceTest
java.io.IOException: Stream closed
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.001 sec - in tests.CostesSignificanceTest
Running tests.LiICQTest
java.io.IOException: Stream closed
java.io.IOException: Stream closed
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 sec - in tests.LiICQTest

Results :

Tests run: 29, Failures: 0, Errors: 0, Skipped: 22

[INFO] 
[INFO] --- maven-jar-plugin:2.5:jar (default-jar) @ Colocalisation_Analysis ---
[INFO] Building jar: /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT.jar
[INFO] 
[INFO] >>> maven-source-plugin:2.3:jar (default) @ Colocalisation_Analysis >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ Colocalisation_Analysis ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO]   Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO]   Adding ignore: com/kenai/constantine/*
[INFO]   Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO]   Adding ignore: jnr/ffi/*
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ Colocalisation_Analysis ---
[INFO] 
[INFO] --- scijava-maven-plugin:0.2.0:set-rootdir (set-rootdir) @ Colocalisation_Analysis ---
[INFO] 
[INFO] <<< maven-source-plugin:2.3:jar (default) @ Colocalisation_Analysis <<<
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar (default) @ Colocalisation_Analysis ---
[INFO] Building jar: /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] >>> maven-source-plugin:2.3:jar (attach-sources) @ Colocalisation_Analysis >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ Colocalisation_Analysis ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO]   Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO]   Adding ignore: com/kenai/constantine/*
[INFO]   Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO]   Adding ignore: jnr/ffi/*
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ Colocalisation_Analysis ---
[INFO] 
[INFO] --- scijava-maven-plugin:0.2.0:set-rootdir (set-rootdir) @ Colocalisation_Analysis ---
[INFO] 
[INFO] <<< maven-source-plugin:2.3:jar (attach-sources) @ Colocalisation_Analysis <<<
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar (attach-sources) @ Colocalisation_Analysis ---
[WARNING] Artifact sc.fiji:Colocalisation_Analysis:java-source:sources:2.0.1-SNAPSHOT already attached to project, ignoring duplicate
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ Colocalisation_Analysis ---
[INFO] 
Loading source file /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/Coloc_2.java...
Loading source file /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/ColocImgLibGadgets.java...
Loading source file /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/Colocalisation_Test.java...
Loading source file /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/Colocalisation_Threshold.java...
Loading source files for package algorithms...
Loading source files for package gadgets...
Loading source files for package net.imglib2...
Loading source files for package net.imglib2.predicate...
Loading source files for package net.imglib2.algorithm.math...
Loading source files for package results...
Constructing Javadoc information...
Standard Doclet version 1.6.0_45
Building tree for all the packages and classes...
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Building index for all the packages and classes...
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17 warnings
[WARNING] Javadoc Warnings
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/Coloc_2.java:395: warning - @param argument "maskBB" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/CostesSignificanceTest.java:238: warning - @param argument "outOfBoundsFactory" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/CostesSignificanceTest.java:281: warning - @param argument "outOfBoundsFactory" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/CostesSignificanceTest.java:281: warning - @param argument "forceOutOfBounds" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/CostesSignificanceTest.java:311: warning - @param argument "outOfBoundsFactory" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/CostesSignificanceTest.java:311: warning - @param argument "forceOutOfBounds" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/Histogram2D.java:303: warning - @param argument "ch1BinWidt" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/Histogram2D.java:313: warning - @param argument "ch2BinWidt" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/PearsonsCorrelation.java:38: warning - @param argument "theImplementation" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/PearsonsCorrelation.java:235: warning - @param argument "img1" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/PearsonsCorrelation.java:235: warning - @param argument "img2" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/PearsonsCorrelation.java:288: warning - @param argument "img1" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/PearsonsCorrelation.java:288: warning - @param argument "img2" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/algorithms/SpearmanRankCorrelation.java:191: warning - @param argument "rankedVals" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/net/imglib2/algorithm/math/ImageStatistics.java:53: warning - @param argument "mask" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/results/PDFWriter.java:127: warning - @param argument "img" is not a parameter name.
[WARNING] /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/src/main/java/results/PDFWriter.java:127: warning - @param argument "printName" is not a parameter name.
[INFO] Fixed Javadoc frame injection vulnerability (CVE-2013-1571) in 1 files.
[INFO] Building jar: /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.5:test-jar (default) @ Colocalisation_Analysis ---
[INFO] Building jar: /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT-tests.jar
[INFO] 
[INFO] --- maven-install-plugin:2.5.1:install (default-install) @ Colocalisation_Analysis ---
[INFO] Installing /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT.jar to /var/lib/jenkins/.m2/repository/sc/fiji/Colocalisation_Analysis/2.0.1-SNAPSHOT/Colocalisation_Analysis-2.0.1-SNAPSHOT.jar
[INFO] Installing /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/pom.xml to /var/lib/jenkins/.m2/repository/sc/fiji/Colocalisation_Analysis/2.0.1-SNAPSHOT/Colocalisation_Analysis-2.0.1-SNAPSHOT.pom
[INFO] Installing /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT-sources.jar to /var/lib/jenkins/.m2/repository/sc/fiji/Colocalisation_Analysis/2.0.1-SNAPSHOT/Colocalisation_Analysis-2.0.1-SNAPSHOT-sources.jar
[INFO] Installing /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT-javadoc.jar to /var/lib/jenkins/.m2/repository/sc/fiji/Colocalisation_Analysis/2.0.1-SNAPSHOT/Colocalisation_Analysis-2.0.1-SNAPSHOT-javadoc.jar
[INFO] Installing /data/devel/jenkins/jobs/Colocalisation_Analysis/workspace/target/Colocalisation_Analysis-2.0.1-SNAPSHOT-tests.jar to /var/lib/jenkins/.m2/repository/sc/fiji/Colocalisation_Analysis/2.0.1-SNAPSHOT/Colocalisation_Analysis-2.0.1-SNAPSHOT-tests.jar
[INFO] 
[INFO] --- imagej-maven-plugin:0.5.4:copy-jars (copy-jars) @ Colocalisation_Analysis ---
[INFO] Property 'imagej.app.directory' unset; Skipping copy-jars
[INFO] 
[INFO] --- maven-deploy-plugin:2.8.1:deploy (default-deploy) @ Colocalisation_Analysis ---
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 12.340s
[INFO] Finished at: Wed Nov 05 21:59:15 CST 2014
[INFO] Final Memory: 22M/340M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-deploy-plugin:2.8.1:deploy (default-deploy) on project Colocalisation_Analysis: Deployment failed: repository element was not specified in the POM inside distributionManagement element or in -DaltDeploymentRepository=id::layout::url parameter -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
Build step 'Execute shell' marked build as failure
Archiving artifacts