[ImageJ-builds] Build failed in Jenkins: TrackMate #11

Mon Jan 13 09:32:26 CST 2014

See <http://jenkins.imagej.net/job/TrackMate/11/changes>

Changes:

[Jean-Yves Tinevez] TrackMate_: start developing v2.2.0

[Jean-Yves Tinevez] TrackMate_: put check input logic where it won't interfere with scripting

[Jean-Yves Tinevez] TrackMate_: fix the virtual empty image

[Jean-Yves Tinevez] TrackMate_: add an action that can merge data from another file

[Jean-Yves Tinevez] TrackMate_: fix missing edge features computation in process() method

[Jean-Yves Tinevez] TrackMate_: basic key handling in TrackScheme

[Jean-Yves Tinevez] TrackMate_: fiddle with the new imglib2meta package

[Jean-Yves Tinevez] TrackMate_: the tracks can be navigated through  using the keyboard in TrackScheme

[Jean-Yves Tinevez] TrackMate_: fix inconsistency in the row headers of TrackScheme

[Jean-Yves Tinevez] TrackMate_: fix performance clog when selecting/deselecting in TrackScheme

[Jean-Yves Tinevez] TrackMate_: fix NPE when loading at the spot filtering state

[Jean-Yves Tinevez] TrackMate_: make the track analyzers stateless.

[Jean-Yves Tinevez] TrackMate_: make the edge analyzers stateless.

[Jean-Yves Tinevez] TrackMate_: make the spot analyzer factories stateless.

[Jean-Yves Tinevez] TrackMate_: make the action provider stateles

[Jean-Yves Tinevez] TrackMate_: make the export action more easily reusable.

[Jean-Yves Tinevez] TrackMate_: deal gracefully with ImagePlus created ex nihilo

[Jean-Yves Tinevez] TrackMate_: blank constructor for DetectorProvider

[Jean-Yves Tinevez] TrackMate_: use a blank constructor for TrackerProvider

[Jean-Yves Tinevez] TrackMate_: make the view provider stateless

[Jean-Yves Tinevez] TrackMate_: use a simpler way to register new feature analyzer in the GUI

[Jean-Yves Tinevez] TrackMate_: re-enable the track duration analyzer

[Jean-Yves Tinevez] TrackMate_: setting the tracks in bulk must be made through the model

[Jean-Yves Tinevez] TrackMate_: prevents NPE when using the 3D viewer as main view.

[Jean-Yves Tinevez] TrackMate_: fix longstanding bug with 3D viewer

[Jean-Yves Tinevez] TrackMate_: prompt the user for 8-bit conversion...

[Jean-Yves Tinevez] TrackMate_: the 3D viewer correctly reports spot removal

[Jean-Yves Tinevez] TrackMate_: the 3D viewer correctly reports spot additions

[Jean-Yves Tinevez] TrackMate_: fix ModelChangeEvent tests

[Jean-Yves Tinevez] TrackMate_: the 3D viewer now reports spot modification correctly

[Jean-Yves Tinevez] TrackMate_: the 3D viewer now echoes any model change

[Jean-Yves Tinevez] TrackMate_: fix recent TrackScheme layout refreshing bug

[Jean-Yves Tinevez] TrackMate_: use the streamlined version of imglib2 again

[Jean-Yves Tinevez] TrackMate_: use the new FFTConvolution in the LogDetector

[Jean-Yves Tinevez] TrackMate_: fix a serious mistake in LoG.

[Jean-Yves Tinevez] TrackMate_: use Tobias DoG implementation.

[Jean-Yves Tinevez] TrackMate_: put back the old DogDetector implementation.

[Jean-Yves Tinevez] TrackMate_: Directly compute and use a LoG kernel.

[Jean-Yves Tinevez] TrackMate_: playing and finding problems with the new imglib2 tools

[Jean-Yves Tinevez] TrackMate_: more fiddling with the new FFTConvolution.

[Jean-Yves Tinevez] TrackMate_: performance test of the new DoG detector.

[Jean-Yves Tinevez] TrackMate_: use the new imglib2 local extrema finder in LoG detector

[Jean-Yves Tinevez] TrackMate_: multithreaded tests for the new LoG detector

[Jean-Yves Tinevez] TrackMate_: implement and use the new DoG detector.

[Jean-Yves Tinevez] TrackMate_: code style change.

[Jean-Yves Tinevez] TrackMate_: DoG: use the threshold early.

[Jean-Yves Tinevez] TrackMate_: code style change.

[Jean-Yves Tinevez] TrackMate_: add a method to provide functionality in the GUI,

[Jean-Yves Tinevez] TrackMate_: code style changes.

[Jean-Yves Tinevez] TrackMate_: add clear() to SpotCollection.

[Jean-Yves Tinevez] TrackMate_: code style changes.

[Jean-Yves Tinevez] TrackMate_: add methods to clear the tracks of the model.

[Jean-Yves Tinevez] TrackMate_: navigating backward clears the model.

[Jean-Yves Tinevez] TrackMate_: code style changes.

[Jean-Yves Tinevez] TrackMate_: change the way the ROI is used internally.

[Jean-Yves Tinevez] TrackMate_: code style changes.

[Jean-Yves Tinevez] TrackMate_: rewrite the median filter.

[Jean-Yves Tinevez] TrackMate_: code style changes.

[Jean-Yves Tinevez] TrackMate_: fix bug in edge analyzer provider.

[Jean-Yves Tinevez] TrackMate_: update the semi-auto tracking.

[Jean-Yves Tinevez] TrackMate_: remove now useless class.

[Jean-Yves Tinevez] TrackMate_: remove useless methods and classes.

[Jean-Yves Tinevez] TrackMate_: move interactive tests out of the main folder

[Jean-Yves Tinevez] TrackMate_: explicit generation of LoG kernels.

[Jean-Yves Tinevez] TrackMate_: fix several serious problems with the LoG kernel.

[Jean-Yves Tinevez] TrackMate_: performance tests for new detectors.

[Jean-Yves Tinevez] TrackMate_: remove useless method type parameter.

[Jean-Yves Tinevez] TrackMate_: fix the semi-auto tracking.

[Jean-Yves Tinevez] TrackMate_: code style changes.

[Jean-Yves Tinevez] TrackMate_: add a drawing depth display setting.

[Jean-Yves Tinevez] TrackMate_: performance tweaks for the tracks display.

[Jean-Yves Tinevez] TrackMate_: performance tweak for the track colorer.

[Jean-Yves Tinevez] TrackMate_: use jdom2 2.0.5, again.

[Jean-Yves Tinevez] Temporary manually enforce jdom 2.0.5.

[Jean-Yves Tinevez] Ensure we never write incomplete track data to XML.

[Jean-Yves Tinevez] Remove some eclipse warnings.

[Jean-Yves Tinevez] Code style changes.

[Jean-Yves Tinevez] Simplify Spot constructors.

[Jean-Yves Tinevez] Spot: enforce the specification of x, y, z, radius and quality.

[Jean-Yves Tinevez] Ignore by-products of the fiji pom.xml.

[Jean-Yves Tinevez] Fix Array out of bounds when detecting in 2D images.

[Jean-Yves Tinevez] Change the name of nested class to avoid confusion.

[Jean-Yves Tinevez] Git ignore mire stuff.

[Jean-Yves Tinevez] Assume TrackMate and fiji source live in the same folder.

[Jean-Yves Tinevez] Fix generic type conflict in interactive test.

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Un changement dans la base de code a provoqué le lancement de ce job
Building on master
Checkout:workspace / <http://jenkins.imagej.net/job/TrackMate/ws/> - hudson.remoting.LocalChannel at 6059906f
Using strategy: Default
Last Built Revision: Revision a19afa71a8aa0a9957f957af0bb6341813f8c0a7 (origin/master)
Fetching changes from 1 remote Git repository
Fetching upstream changes from git://github.com/fiji/TrackMate
Commencing build of Revision 83507b4eafeabe1266273128376389ef2cbf2108 (origin/master)
Checking out Revision 83507b4eafeabe1266273128376389ef2cbf2108 (origin/master)
[workspace] $ /bin/sh -xe /tmp/hudson6105038779931065647.sh
+ git clean -dfx
Removing target/
[workspace] $ /bin/sh -xe /tmp/hudson4184994641214844147.sh
+ mvn -DupdateReleaseInfo=true deploy
Picked up JAVA_TOOL_OPTIONS: -Dfile.encoding=UTF-8
[INFO] Scanning for projects...
[INFO] snapshot sc.fiji:pom-fiji:2.0.0-SNAPSHOT: checking for updates from imagej.releases
[INFO] snapshot sc.fiji:pom-fiji:2.0.0-SNAPSHOT: checking for updates from imagej.snapshots
[WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = '5d1b7b85d1c205ec902e963f4ff736a031e0ed20'; remote = '2a746d574f513e304d53ca5fb3c85e2970a7f133' - RETRYING
[WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = '5d1b7b85d1c205ec902e963f4ff736a031e0ed20'; remote = '2a746d574f513e304d53ca5fb3c85e2970a7f133' - IGNORING
[INFO] ------------------------------------------------------------------------
[INFO] Building plugins/TrackMate_.jar
[INFO]    task-segment: [deploy]
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[INFO] [buildnumber:create {execution: default}]
[INFO] Checking for local modifications: skipped.
[INFO] Updating project files from SCM: skipped.
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/TrackMate/workspace && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/TrackMate/workspace
[INFO] Storing buildNumber: 83507b4eafeabe1266273128376389ef2cbf2108 at timestamp: 1389627131666
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/TrackMate/workspace && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/TrackMate/workspace
[INFO] Storing buildScmBranch: UNKNOWN
[INFO] [imagej:set-rootdir {execution: set-rootdir}]
[INFO] Setting rootdir: /data/devel/jenkins/jobs/TrackMate/workspace
[debug] execute contextualize
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 63 resources
[INFO] snapshot sc.fiji:pom-fiji-plugins:2.0.0-SNAPSHOT: checking for updates from imagej.releases
[INFO] snapshot sc.fiji:pom-fiji-plugins:2.0.0-SNAPSHOT: checking for updates from imagej.snapshots
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[INFO] snapshot sc.fiji:pom-fiji-plugins:2.0.0-SNAPSHOT: checking for updates from imagej.thirdparty
[WARNING] Overriding profile: 'null' (source: pom) with new instance from source: pom
[WARNING] Overriding profile: 'null' (source: pom) with new instance from source: pom
[WARNING] Overriding profile: 'null' (source: pom) with new instance from source: pom
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Downloading: http://maven.imagej.net/content/repositories/thirdparty/org/jdom/jdom2/2.0.5/jdom2-2.0.5.pom
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[INFO] [compiler:compile {execution: default-compile}]
[INFO] Compiling 243 source files to /data/devel/jenkins/jobs/TrackMate/workspace/target/classes
[debug] execute contextualize
[INFO] [resources:testResources {execution: default-testResources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /data/devel/jenkins/jobs/TrackMate/workspace/src/test/resources
[INFO] [compiler:testCompile {execution: default-testCompile}]
[INFO] Compiling 47 source files to /data/devel/jenkins/jobs/TrackMate/workspace/target/test-classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /data/devel/jenkins/jobs/TrackMate/workspace/src/test/java/fiji/plugin/trackmate/interactivetests/NewLogDetectorTestDrive.java:[46,103] incompatible types; inferred type argument(s) net.imglib2.type.numeric.NumericType<? extends net.imglib2.type.numeric.NumericType<?>> do not conform to bounds of type variable(s) T
found   : <T>net.imglib2.meta.ImgPlus<T>
required: net.imglib2.meta.ImgPlus<? extends net.imglib2.type.numeric.NumericType<? extends net.imglib2.type.numeric.NumericType<?>>>
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Compilation failure
/data/devel/jenkins/jobs/TrackMate/workspace/src/test/java/fiji/plugin/trackmate/interactivetests/NewLogDetectorTestDrive.java:[46,103] incompatible types; inferred type argument(s) net.imglib2.type.numeric.NumericType<? extends net.imglib2.type.numeric.NumericType<?>> do not conform to bounds of type variable(s) T
found   : <T>net.imglib2.meta.ImgPlus<T>
required: net.imglib2.meta.ImgPlus<? extends net.imglib2.type.numeric.NumericType<? extends net.imglib2.type.numeric.NumericType<?>>>

[INFO] ------------------------------------------------------------------------
[INFO] For more information, run Maven with the -e switch
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 18 seconds
[INFO] Finished at: Mon Jan 13 09:32:26 CST 2014
[INFO] Final Memory: 80M/884M
[INFO] ------------------------------------------------------------------------
Build step 'Exécuter un script shell' marked build as failure
Archiving artifacts