[ImageJ-builds] Build failed in Jenkins: Fiji-Maven #228

Wed Jan 9 10:06:32 CST 2013

See <http://jenkins.imagej.net/job/Fiji-Maven/228/>

------------------------------------------
[...truncated 7246 lines...]
[INFO] plugins/Dichromacy_.jar ............................... SUCCESS [0.615s]
[INFO] plugins/Differentials_.jar ............................ SUCCESS [0.700s]
[INFO] plugins/Directionality_.jar ........................... SUCCESS [1.524s]
[INFO] jars/imageware.jar .................................... SUCCESS [2.745s]
[INFO] jars/wavelets.jar ..................................... SUCCESS [1.208s]
[INFO] plugins/Extended_Depth_Field.jar ...................... SUCCESS [1.685s]
[INFO] plugins/FS_Align_TrakEM2.jar .......................... SUCCESS [4.845s]
[INFO] jars/imagescience.jar ................................. SUCCESS [4.017s]
[INFO] plugins/FeatureJ_.jar ................................. SUCCESS [0.895s]
[INFO] plugins/Feature_Detection.jar ......................... SUCCESS [0.798s]
[INFO] jars/fake.jar ......................................... SUCCESS [1.595s]
[INFO] plugins/JRuby_Interpreter.jar ......................... SUCCESS [0.894s]
[INFO] plugins/Javascript_.jar ............................... SUCCESS [0.729s]
[INFO] plugins/Jython_Interpreter.jar ........................ SUCCESS [0.805s]
[INFO] plugins/Refresh_Javas.jar ............................. SUCCESS [0.864s]
[INFO] plugins/Script_Editor.jar ............................. SUCCESS [2.151s]
[INFO] plugins/Fiji_Developer.jar ............................ SUCCESS [1.380s]
[INFO] plugins/Fiji_Package_Maker.jar ........................ SUCCESS [3.270s]
[INFO] plugins/FlowJ_.jar .................................... SUCCESS [2.246s]
[INFO] plugins/Graph_Cut.jar ................................. SUCCESS [1.229s]
[INFO] plugins/Gray_Morphology.jar ........................... SUCCESS [0.844s]
[INFO] plugins/Helmholtz_Analysis.jar ........................ SUCCESS [0.773s]
[INFO] plugins/IJ_Robot.jar .................................. SUCCESS [0.625s]
[INFO] plugins/IO_.jar ....................................... SUCCESS [1.776s]
[INFO] jars/jep.jar .......................................... SUCCESS [3.955s]
[INFO] plugins/Image_Expression_Parser.jar ................... SUCCESS [1.778s]
[INFO] plugins/Interactive_3D_Surface_Plot.jar ............... SUCCESS [1.337s]
[INFO] plugins/IsoData_Classifier.jar ........................ SUCCESS [0.608s]
[INFO] plugins/Kuwahara_Filter.jar ........................... SUCCESS [0.610s]
[INFO] plugins/LSM_Reader.jar ................................ SUCCESS [2.430s]
[INFO] plugins/LSM_Toolbox.jar ............................... SUCCESS [1.661s]
[INFO] plugins/Lasso_and_Blow_Tool.jar ....................... SUCCESS [0.674s]
[INFO] plugins/Linear_Kuwahara.jar ........................... SUCCESS [0.625s]
[INFO] plugins/LocalThickness_.jar ........................... SUCCESS [0.776s]
[INFO] plugins/MTrack2_.jar .................................. SUCCESS [0.710s]
[INFO] plugins/MTrackJ_.jar .................................. SUCCESS [1.535s]
[INFO] plugins/M_I_P.jar ..................................... SUCCESS [0.722s]
[INFO] plugins/Manual_Tracking.jar ........................... SUCCESS [1.106s]
[INFO] plugins/MosaicJ_.jar .................................. SUCCESS [1.347s]
[INFO] plugins/Multi_Kymograph.jar ........................... SUCCESS [0.695s]
[INFO] plugins/PIV_analyser.jar .............................. SUCCESS [0.790s]
[INFO] plugins/PointPicker_.jar .............................. SUCCESS [0.935s]
[INFO] plugins/QuickPALM_.jar ................................ SUCCESS [1.017s]
[INFO] plugins/RATS_.jar ..................................... SUCCESS [0.760s]
[INFO] plugins/RandomJ_.jar .................................. SUCCESS [0.780s]
[INFO] plugins/Reconstruct_Reader.jar ........................ SUCCESS [1.781s]
[INFO] plugins/Samples_.jar .................................. SUCCESS [0.259s]
[INFO] plugins/Scala_Interpreter.jar ......................... SUCCESS [3.927s]
[INFO] plugins/Series_Labeler.jar ............................ SUCCESS [0.891s]
[INFO] plugins/SheppLogan_.jar ............................... SUCCESS [0.649s]
[INFO] plugins/Skeletonize3D_.jar ............................ SUCCESS [0.718s]
[INFO] plugins/VIB_.jar ...................................... SUCCESS [2.637s]
[INFO] plugins/Simple_Neurite_Tracer.jar ..................... SUCCESS [4.299s]
[INFO] plugins/Siox_Segmentation.jar ......................... SUCCESS [1.562s]
[INFO] plugins/Snakuscule_.jar ............................... SUCCESS [1.045s]
[INFO] plugins/SplineDeformationGenerator_.jar ............... SUCCESS [1.046s]
[INFO] plugins/StackReg_.jar ................................. SUCCESS [0.944s]
[INFO] plugins/Stack_Manipulation.jar ........................ SUCCESS [0.940s]
[INFO] plugins/Statistical_Region_Merging.jar ................ SUCCESS [0.670s]
[INFO] plugins/Sync_Win.jar .................................. SUCCESS [1.133s]
[INFO] plugins/Thread_Killer.jar ............................. SUCCESS [0.593s]
[INFO] plugins/Threshold_Colour.jar .......................... SUCCESS [0.908s]
[INFO] plugins/Time_Stamper.jar .............................. SUCCESS [0.740s]
[INFO] plugins/ToAST_.jar .................................... SUCCESS [0.953s]
[INFO] plugins/TopoJ_.jar .................................... SUCCESS [0.671s]
[INFO] plugins/TrackMate_.jar ................................ SUCCESS [3.812s]
[INFO] plugins/Trainable_Segmentation.jar .................... SUCCESS [3.106s]
[INFO] plugins/TransformJ_.jar ............................... SUCCESS [1.044s]
[INFO] plugins/TurboReg_.jar ................................. SUCCESS [1.460s]
[INFO] plugins/UnwarpJ_.jar .................................. SUCCESS [1.561s]
[INFO] jars/Updater_Fix.jar .................................. SUCCESS [0.669s]
[INFO] plugins/Vaa3d_Reader.jar .............................. SUCCESS [1.388s]
[INFO] plugins/Video_Editing.jar ............................. SUCCESS [0.779s]
[INFO] plugins/View5D_.jar ................................... SUCCESS [1.983s]
[INFO] plugins/Volume_Calculator.jar ......................... SUCCESS [2.477s]
[INFO] plugins/Volume_Viewer.jar ............................. SUCCESS [1.652s]
[INFO] plugins/bUnwarpJ_.jar ................................. SUCCESS [1.922s]
[INFO] plugins/blockmatching_.jar ............................ SUCCESS [1.523s]
[INFO] jars/javac.jar ........................................ SUCCESS [5.215s]
[INFO] jars/mij.jar .......................................... SUCCESS [0.733s]
[INFO] plugins/panorama_.jar ................................. SUCCESS [0.950s]
[INFO] plugins/register_virtual_stack_slices.jar ............. SUCCESS [1.629s]
[INFO] plugins/registration_3d.jar ........................... SUCCESS [0.956s]
[INFO] jars/weave_jy2java.jar ................................ SUCCESS [0.984s]
[INFO] Aggregator project for the Fiji submodules ............ SUCCESS [0.114s]
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3 minutes 10 seconds
[INFO] Finished at: Wed Jan 09 10:05:56 CST 2013
[INFO] Final Memory: 138M/5119M
[INFO] ------------------------------------------------------------------------
[workspace] $ /bin/sh -xe /tmp/hudson3044059817734250564.sh
+ bin/incremental-deploy.sh
[/tmp/precompiled.1.jar]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
Deploying modules/
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building Aggregator project for the Fiji submodules
[INFO]    task-segment: [deploy]
[INFO] ------------------------------------------------------------------------
[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/Fiji-Maven/workspace/modules && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/Fiji-Maven/workspace/modules
[INFO] Storing buildNumber: 12d47a22313b787697ed132def5da1bd91a83286 at timestamp: 1357747559852
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/Fiji-Maven/workspace/modules && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/Fiji-Maven/workspace/modules
[INFO] Storing buildScmBranch: UNKNOWN
[INFO] [imagej:set-rootdir {execution: set-rootdir}]
[INFO] Setting rootdir: /data/devel/jenkins/jobs/Fiji-Maven/workspace
[INFO] [site:attach-descriptor {execution: default-attach-descriptor}]
[INFO] Preparing source:jar
[WARNING] Removing: jar from forked lifecycle, to prevent recursive invocation.
[INFO] [buildnumber:create {execution: default}]
[INFO] [imagej:set-rootdir {execution: set-rootdir}]
[INFO] [source:jar {execution: default}]
[INFO] [install:install {execution: default-install}]
[INFO] Installing /data/devel/jenkins/jobs/Fiji-Maven/workspace/modules/pom.xml to /var/lib/jenkins/.m2/repository/sc/fiji/pom-fiji-submodules/2.0.0-SNAPSHOT/pom-fiji-submodules-2.0.0-SNAPSHOT.pom
[INFO] [imagej:copy-jars {execution: copy-jars}]
[INFO] [deploy:deploy {execution: default-deploy}]
[INFO] Retrieving previous build number from imagej.snapshots
Uploading: http://maven.imagej.net/content/repositories/snapshots/sc/fiji/pom-fiji-submodules/2.0.0-SNAPSHOT/pom-fiji-submodules-2.0.0-20130109.160602-2.pom
Jan 9, 2013 10:06:02 AM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
2/2K
2K uploaded  (pom-fiji-submodules-2.0.0-20130109.160602-2.pom)
[INFO] Retrieving previous metadata from imagej.snapshots
[INFO] Uploading repository metadata for: 'artifact sc.fiji:pom-fiji-submodules'
Jan 9, 2013 10:06:03 AM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
[INFO] Retrieving previous metadata from imagej.snapshots
[INFO] Uploading repository metadata for: 'snapshot sc.fiji:pom-fiji-submodules:2.0.0-SNAPSHOT'
Jan 9, 2013 10:06:03 AM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5 seconds
[INFO] Finished at: Wed Jan 09 10:06:03 CST 2013
[INFO] Final Memory: 55M/1016M
[INFO] ------------------------------------------------------------------------
[/tmp/precompiled.1.jar]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
Deploying native/FFMPEG_IO/ffmpeg/
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building FFMPEG
[INFO]    task-segment: [deploy]
[INFO] ------------------------------------------------------------------------
[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/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg
[INFO] Storing buildNumber: 12d47a22313b787697ed132def5da1bd91a83286 at timestamp: 1357747566368
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg
[INFO] Storing buildScmBranch: UNKNOWN
[INFO] [imagej:set-rootdir {execution: set-rootdir}]
[INFO] Setting rootdir: /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO
[debug] execute contextualize
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg/src/main/resources
[INFO] [compiler:compile {execution: default-compile}]
[INFO] Compiling 2 source files to /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg/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/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg/src/test/resources
[INFO] [compiler:testCompile {execution: default-testCompile}]
[INFO] No sources to compile
[INFO] [surefire:test {execution: default-test}]
[INFO] No tests to run.
[INFO] Surefire report directory: /data/devel/jenkins/jobs/Fiji-Maven/workspace/native/FFMPEG_IO/ffmpeg/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

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

[INFO] Preparing exec:java
[WARNING] Removing: java from forked lifecycle, to prevent recursive invocation.
[INFO] [buildnumber:create {execution: default}]
[INFO] [imagej:set-rootdir {execution: set-rootdir}]
[INFO] [exec:java {execution: default}]
Cloning into 'ffmpeg'...
Note: checking out '6c3d021891a942403eb644eae0e6378a0dcf8b3c'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 6c3d021... Properly add HAVE_YASM around yasmified symbols. Should fix compile error on configurations using --disable-yasm.
yasm not found, use --disable-yasm for a crippled build

If you think configure made a mistake, make sure you are using the latest
version from SVN.  If the latest version fails, report the problem to the
ffmpeg-user at mplayerhq.hu mailing list or IRC #ffmpeg on irc.freenode.net.
Include the log file "config.log" produced by configure as this will help
solving the problem.
[WARNING] 
java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.RuntimeException: exit status 1: [./configure, --enable-gpl, --enable-shared, --extra-ldflags=-m64 -Wl,-rpath,\\\$\$\$\$ORIGIN/, --extra-cflags=-m64]
java.io.PrintStream at 64f007ad
	at imagej.util.ProcessUtils.exec(ProcessUtils.java:95)
	at imagej.util.FileUtils.exec(FileUtils.java:412)
	at fiji.ffmpeg.CompileFFMPEG.exec(CompileFFMPEG.java:135)
	at fiji.ffmpeg.CompileFFMPEG.main(CompileFFMPEG.java:65)
	... 6 more
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD ERROR
[INFO] ------------------------------------------------------------------------
[INFO] An exception occured while executing the Java class. null

exit status 1: [./configure, --enable-gpl, --enable-shared, --extra-ldflags=-m64 -Wl,-rpath,\\\$\$\$\$ORIGIN/, --extra-cflags=-m64]
java.io.PrintStream at 64f007ad
[INFO] ------------------------------------------------------------------------
[INFO] For more information, run Maven with the -e switch
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 27 seconds
[INFO] Finished at: Wed Jan 09 10:06:31 CST 2013
[INFO] Final Memory: 52M/1029M
[INFO] ------------------------------------------------------------------------
Build step 'Execute shell' marked build as failure