[ImageJ-builds] Build failed in Jenkins: fiji-core #455
Jenkins Daemon
jenkins at qa.nest-initiative.org
Thu Aug 9 16:13:42 CDT 2012
See <https://qa.nest-initiative.org/job/fiji-core/455/changes>
Changes:
[stephan.preibisch] Updated GUI to ask for blockSize, where to compute and removed old questions that do not apply anymore
[stephan.preibisch] Removed import
[stephan.preibisch] Generalizing convolution so that it can execute different ways to convolve images
[stephan.preibisch] Can compute the convolution in blocks to use less memory or cuda
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plugins/Linear_Kuwahara.jar done
Czechsummer (jars/imglib-scripting.jar)
jars/imglib-scripting.jar done
Czechsummer (plugins/Samples_.jar)
plugins/Samples_.jar done
Czechsummer (jars/mij.jar)
jars/mij.jar done
Czechsummer (jars/weave_jy2java.jar)
jars/weave_jy2java.jar done
Czechsummer (plugins/3D_Blob_Segmentation.jar)
plugins/3D_Blob_Segmentation.jar done
Czechsummer (plugins/Feature_Detection.jar)
plugins/Feature_Detection.jar done
Czechsummer (plugins/Lasso_and_Blow_Tool.jar)
plugins/Lasso_and_Blow_Tool.jar done
Czechsummer (plugins/Thread_Killer.jar)
plugins/Thread_Killer.jar done
Czechsummer (plugins/Dichromacy_.jar)
plugins/Dichromacy_.jar done
Czechsummer (plugins/Colour_Deconvolution.jar)
plugins/Colour_Deconvolution.jar done
Czechsummer (plugins/Threshold_Colour.jar)
plugins/Threshold_Colour.jar done
Czechsummer (jars/imglib2-ui.jar)
jars/imglib2-ui.jar done
Czechsummer (Contents/MacOS/fiji-macosx)
Contents/MacOS/fiji-macosx done
Czechsummer (Contents/MacOS/fiji-tiger)
Contents/MacOS/fiji-tiger done
Czechsummer (plugins/blockmatching_.jar)
plugins/blockmatching_.jar done
Czechsummer (jars/imglib2-algorithms-gpl.jar)
jars/imglib2-algorithms-gpl.jar done
Czechsummer (jars/jgraphx.jar)
jars/jgraphx.jar done
Czechsummer (jars/jdom-contrib.jar)
jars/jdom-contrib.jar done
Czechsummer (jars/jgrapht-jdk1.6.jar)
jars/jgrapht-jdk1.6.jar done
Czechsummer (jars/jdom.jar)
jars/jdom.jar done
Czechsummer (plugins/TrackMate_.jar)
plugins/TrackMate_.jar done
Done: Czechsummer
Could not update due to conflicts:
plugins/bUnwarpJ_.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
plugins/register_virtual_stack_slices.jar, plugins/TrakEM2_.jar
plugins/Image_5D.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/imagescience.jar, plugins/Sync_Win.jar
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jars/loci-common-4.4-SNAPSHOT.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
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plugins/Fiji_Developer.jar, plugins/Stitching_.jar
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plugins/Trainable_Segmentation.jar
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plugins/TrakEM2_.jar, plugins/Script_Editor.jar, plugins/Simple_Neurite_Tracer.jar, jars/imglib-scripting.jar, plugins/TrackMate_.jar
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plugins/Script_Editor.jar, jars/weave_jy2java.jar
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jars/VIB-lib.jar, plugins/3D_Viewer.jar, plugins/TrakEM2_.jar, jars/imglib-ij.jar, plugins/Script_Editor.jar, plugins/Stitching_.jar, jars/imglib-algorithms.jar, plugins/Trainable_Segmentation.jar, plugins/Algorithm_Launcher.jar, plugins/Image_Expression_Parser.jar, jars/imglib-scripting.jar, plugins/Feature_Detection.jar, plugins/TrackMate_.jar
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plugins/VIB_.jar, plugins/3D_Viewer.jar, plugins/TrakEM2_.jar, plugins/Trainable_Segmentation.jar, plugins/Simple_Neurite_Tracer.jar
jars/fiji-scripting.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
plugins/Refresh_Javas.jar, plugins/Javascript_.jar, plugins/Jython_Interpreter.jar, plugins/JRuby_Interpreter.jar, plugins/Clojure_Interpreter.jar, plugins/BeanShell_Interpreter.jar, plugins/Script_Editor.jar, plugins/CLI_.jar, jars/weave_jy2java.jar
jars/ome-xml-4.4-SNAPSHOT.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/scifio-4.4-SNAPSHOT.jar, jars/imglib2-io-2.0.0-SNAPSHOT.jar
jars/autocomplete.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
plugins/Script_Editor.jar
jars/jcommon-1.0.17.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/jfreechart-1.0.14.jar, plugins/TrakEM2_.jar, plugins/Script_Editor.jar, plugins/Simple_Neurite_Tracer.jar, jars/imglib-scripting.jar, plugins/TrackMate_.jar
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plugins/CLI_.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
plugins/Script_Editor.jar
jars/jai_imageio-4.4-SNAPSHOT.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/scifio-4.4-SNAPSHOT.jar
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jars/VIB-lib.jar, plugins/VIB_.jar, plugins/Simple_Neurite_Tracer.jar
jars/junit-4.8.1.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/jython.jar, jars/edu_mines_jtk.jar, jars/VIB-lib.jar, plugins/VIB_.jar, plugins/Simple_Neurite_Tracer.jar, jars/jep.jar, plugins/Image_Expression_Parser.jar
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plugins/blockmatching_.jar
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plugins/Script_Editor.jar
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jars/scifio-4.4-SNAPSHOT.jar
jars/imglib-algorithms.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
plugins/Stitching_.jar, plugins/Trainable_Segmentation.jar, plugins/Image_Expression_Parser.jar, jars/imglib-scripting.jar, plugins/Feature_Detection.jar, plugins/TrackMate_.jar
jars/itextpdf.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/jpedalSTD.jar, plugins/IO_.jar, plugins/TrackMate_.jar
jars/Jama.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/imglib.jar, jars/VIB-lib.jar, plugins/3D_Viewer.jar, plugins/VIB_.jar, plugins/TrakEM2_.jar, jars/VectorString.jar, jars/imglib-algorithms.jar, jars/jep.jar, plugins/Feature_Detection.jar, plugins/TrackMate_.jar
jars/javassist-3.16.1-GA.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
jars/fiji-compat.jar
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plugins/Bug_Submitter.jar
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plugins/AnalyzeSkeleton_.jar, plugins/Analyze_Reader_Writer.jar, plugins/Bug_Submitter.jar, plugins/Fiji_Updater.jar, plugins/Color_Inspector_3D.jar, plugins/FlowJ_.jar, plugins/Gray_Morphology.jar, plugins/IO_.jar, plugins/Interactive_3D_Surface_Plot.jar, plugins/M_I_P.jar, plugins/SplineDeformationGenerator_.jar, plugins/Stack_Manipulation.jar, plugins/ToAST_.jar, plugins/Image_5D.jar, jars/imagescience.jar, plugins/TransformJ_.jar, plugins/TurboReg_.jar, plugins/VIB_.jar, jars/VIB-lib.jar, jars/imglib.jar, plugins/mpicbg_.jar, plugins/3D_Viewer.jar, plugins/Volume_Viewer.jar, plugins/ij-ImageIO_.jar, plugins/level_sets.jar, plugins/bUnwarpJ_.jar, plugins/TrakEM2_.jar, jars/imglib-ij.jar, plugins/register_virtual_stack_slices.jar, plugins/Calculator_Plus.jar, plugins/Sync_Win.jar, plugins/3D_Objects_Counter.jar, plugins/LocalThickness_.jar, jars/VectorString.jar, plugins/Fiji_Plugins.jar, jars/fiji-scripting.jar, jars/fiji-compat.jar, plugins/Refresh_Javas.jar, plugins/Javascript_.jar, plugins/Jython_Interpreter.jar, plugins/JRuby_Interpreter.jar, plugins/Clojure_Interpreter.jar, plugins/BeanShell_Interpreter.jar, plugins/Script_Editor.jar, plugins/CLI_.jar, plugins/Fiji_Developer.jar, plugins/Trainable_Segmentation.jar, plugins/Stitching_.jar, plugins/Simple_Neurite_Tracer.jar, plugins/Skeletonize3D_.jar, plugins/Algorithm_Launcher.jar, plugins/Anisotropic_Diffusion_2D.jar, plugins/Image_Expression_Parser.jar, plugins/QuickPALM_.jar, plugins/IsoData_Classifier.jar, plugins/MosaicJ_.jar, plugins/StackReg_.jar, plugins/Differentials_.jar, plugins/PointPicker_.jar, plugins/SheppLogan_.jar, plugins/Snakuscule_.jar, plugins/RandomJ_.jar, plugins/Linear_Kuwahara.jar, jars/imglib-scripting.jar, jars/mij.jar, jars/weave_jy2java.jar, plugins/3D_Blob_Segmentation.jar, plugins/Feature_Detection.jar, plugins/Lasso_and_Blow_Tool.jar, plugins/Thread_Killer.jar, plugins/Dichromacy_.jar, plugins/Colour_Deconvolution.jar, plugins/Threshold_Colour.jar, plugins/blockmatching_.jar, jars/imglib2-ij.jar, plugins/TrackMate_.jar
plugins/3D_Viewer.jar: Locally modified and the Updater cannot determine its status. A newer version might be required by
plugins/VIB_.jar, plugins/TrakEM2_.jar, plugins/Fiji_Developer.jar, plugins/Simple_Neurite_Tracer.jar, plugins/3D_Blob_Segmentation.jar, plugins/TrackMate_.jar
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plugins/TransformJ_.jar, plugins/Trainable_Segmentation.jar, plugins/RandomJ_.jar
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plugins/JRuby_Interpreter.jar
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plugins/TrakEM2_.jar, plugins/Script_Editor.jar, plugins/Stitching_.jar, plugins/Trainable_Segmentation.jar, plugins/Image_Expression_Parser.jar, jars/imglib-scripting.jar, plugins/Feature_Detection.jar, plugins/TrackMate_.jar
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plugins/IO_.jar, jars/VIB-lib.jar, plugins/VIB_.jar
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jars/fiji-scripting.jar, plugins/Refresh_Javas.jar, plugins/Script_Editor.jar
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jars/imglib2-io-2.0.0-SNAPSHOT.jar
null: There are files which need to be updated/installed since other files depend on them:
plugins/mpicbg_.jar, jars/imglib2-io-2.0.0-SNAPSHOT.jar, jars/ij-launcher-2.0.0-SNAPSHOT.jar, plugins/TrakEM2_.jar, jars/forms-1.2.1.jar
Checking prerequisites of (fiji.build.SubFake) plugins/Fiji_Plugins.jar <- src-plug...
Parsing src-plugins/Fiji_Plugins/pom.xml
Checking prerequisites of (fiji.build.SubFake) plugins/Color_Inspector_3D.jar <- sr...
Building (fiji.build.SubFake) plugins/Color_Inspector_3D.jar <- sr...
Parsing src-plugins/Color_Inspector_3D/pom.xml
Compiling 4 files in <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D>
[-source, 1.5, -target, 1.5, -classpath, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar,> -d, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/target/classes,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/src/main/java/Color_Inspector_3D.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/src/main/java/SymMat.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/src/main/java/ColorKLT.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/src/main/java/KLT.java]>
using the class path: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>
Note: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Color_Inspector_3D/src/main/java/Color_Inspector_3D.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
plugins/Color_Inspector_3D.jar does not exist yet
Checking prerequisites of (fiji.build.SubFake) plugins/SheppLogan_.jar <- src-plugi...
Building (fiji.build.SubFake) plugins/SheppLogan_.jar <- src-plugi...
Parsing src-plugins/SheppLogan_/pom.xml
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/SheppLogan_>
[-source, 1.5, -target, 1.5, -classpath, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/SheppLogan_/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar,> -d, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/SheppLogan_/target/classes,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/SheppLogan_/src/main/java/SheppLogan_.java]>
using the class path: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/SheppLogan_/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>
Note: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/SheppLogan_/src/main/java/SheppLogan_.java> uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Checking prerequisites of (fiji.build.SubFake) plugins/Differentials_.jar <- src-pl...
Building (fiji.build.SubFake) plugins/Differentials_.jar <- src-pl...
Parsing src-plugins/Differentials_/pom.xml
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Differentials_>
[-source, 1.5, -target, 1.5, -classpath, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Differentials_/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar,> -d, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Differentials_/target/classes,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Differentials_/src/main/java/Differentials_.java]>
using the class path: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Differentials_/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>
Checking prerequisites of (fiji.build.SubFake) plugins/Trainable_Segmentation.jar <...
Building (fiji.build.SubFake) plugins/Trainable_Segmentation.jar <...
Parsing src-plugins/Trainable_Segmentation/pom.xml
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D>
[-source, 1.5, -target, 1.5, -classpath, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar,> -d, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D/target/classes,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D/src/main/java/anisotropic_diffusion/Anisotropic_Diffusion_2D.java]>
using the class path: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>
Compiling 37 files in <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation>
[-source, 1.5, -target, 1.5, -classpath, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/target/classes>:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D/target/Anisotropic_Diffusion_2D-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Fiji_Plugins/target/Fiji_Plugins-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/net/imagej/Image_5D/1.2.5/Image_5D-1.2.5.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Jama/target/Jama-1.0.2.jar>:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Stitching_/target/Stitching_-2.0.0-SNAPSHOT.jar>:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/VIB-lib/target/VIB-lib-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/loci/bio-formats/4.4-SNAPSHOT/bio-formats-4.4-20120306.103639-76.jar:/home/jenkins/.m2/repository/com/sun/clibwrapper_jiio/1.1/clibwrapper_jiio-1.1.jar:/home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/home/jenkins/.m2/repository/org/apache/commons/commons-math/3.0-SNAPSHOT/commons-math-3.0-20120702.214056-1.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/fiji-lib/target/fiji-lib-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/com/jgoodies/forms/1.2.1/forms-1.2.1.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/imagescience/target/imagescience-2.4.0.jar>:/home/jenkins/.m2/repository/mpicbg/imglib/2.0.0-SNAPSHOT/imglib-2.0.0-20120809.051857-553.jar:/home/jenkins/.m2/repository/mpicbg/imglib-algorithms/2.0.0-SNAPSHOT/imglib-algorithms-2.0.0-20120809.051857-553.jar:/home/jenkins/.m2/repository/mpicbg/imglib-ij/2.0.0-SNAPSHOT/imglib-ij-2.0.0-20120809.051857-553.jar:/home/jenkins/.m2/repository/net/imglib2/imglib2/2.0.0-SNAPSHOT/imglib2-2.0.0-20120809.051857-548.jar:/home/jenkins/.m2/repository/net/imglib2/imglib2-algorithms/2.0.0-SNAPSHOT/imglib2-algorithms-2.0.0-20120809.051857-548.jar:/home/jenkins/.m2/repository/net/imglib2/imglib2-ij/2.0.0-SNAPSHOT/imglib2-ij-2.0.0-20120809.051857-545.jar:/home/jenkins/.m2/repository/java3d/j3d-core/1.5.2/j3d-core-1.5.2.jar:/home/jenkins/.m2/repository/java3d/j3d-core-utils/1.5.2/j3d-core-utils-1.5.2.jar:/home/jenkins/.m2/repository/loci/jai_imageio/4.4-SNAPSHOT/jai_imageio-4.4-20120306.103244-82.jar:/home/jenkins/.m2/repository/jama/jama/1.0.2/jama-1.0.2.jar:/home/jenkins/.m2/repository/net/sf/squirrel-sql/thirdparty-non-maven/java-cup/0.11a/java-cup-0.11a.jar:/home/jenkins/.m2/repository/com/jcraft/jsch/0.1.42/jsch-0.1.42.jar:/home/jenkins/.m2/repository/junit/junit/4.5/junit-4.5.jar:/home/jenkins/.m2/repository/com/jcraft/jzlib/1.0.7/jzlib-1.0.7.jar:/home/jenkins/.m2/repository/loci/loci-common/4.4-SNAPSHOT/loci-common-4.4-20120306.103328-82.jar:/home/jenkins/.m2/repository/loci/loci_plugins/4.4-SNAPSHOT/loci_plugins-4.4-20120806.234352-138.jar:/home/jenkins/.m2/repository/log4j/log4j/1.2.14/log4j-1.2.14.jar:/home/jenkins/.m2/repository/loci/lwf-stubs/4.4-SNAPSHOT/lwf-stubs-4.4-20120306.103508-82.jar:/home/jenkins/.m2/repository/loci/mdbtools-java/4.4-SNAPSHOT/mdbtools-java-4.4-20120306.103304-82.jar:/home/jenkins/.m2/repository/loci/metakit/4.4-SNAPSHOT/metakit-4.4-20120306.103417-82.jar:/home/jenkins/.m2/repository/edu/mines/mines-jtk/20100113/mines-jtk-20100113.jar:/home/jenkins/.m2/repository/mpicbg/mpicbg/20120621/mpicbg-20120621.jar:/home/jenkins/.m2/repository/essi-unidata/netcdf-java/4.0.41/netcdf-java-4.0.41.jar:/home/jenkins/.m2/repository/loci/ome-xml/4.4-SNAPSHOT/ome-xml-4.4-20120306.103450-82.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/pal-optimization/target/pal-optimization-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/org/pentaho/pentaho-commons/pentaho-package-manager/1.0.0/pentaho-package-manager-1.0.0.jar:/home/jenkins/.m2/repository/loci/poi-loci/4.4-SNAPSHOT/poi-loci-4.4-20120306.103359-82.jar:/home/jenkins/.m2/repository/loci/scifio/4.4-SNAPSHOT/scifio-4.4-20120316.095357-49.jar:/home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.5.10/slf4j-api-1.5.10.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>:/home/jenkins/.m2/repository/java3d/vecmath/1.5.2/vecmath-1.5.2.jar:/home/jenkins/.m2/repository/nz/ac/waikato/cms/weka/weka-dev/3.7.6/weka-dev-3.7.6.jar, -d, <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/target/classes,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/RandError.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/PixelError.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/ClassificationStatistics.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/Metrics.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/WarpingResults.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/ClusteredWarpingMismatches.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/WarpingError.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/metrics/AdjustedRandError.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/Weka_Segmentation.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/filters/Kuwahara.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/filters/Lipschitz_.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/filters/Entropy_Filter.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/utils/PrincipalComponentAnalysis.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/utils/Utils.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/RoiListOverlay.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/ImageOverlay.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/WekaSegmentation.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/FeatureStack3D.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/Trainable_Segmentation.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/FeatureStack.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/FeatureStackArray.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/InformationGainFunction.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/BalancedRandomForest.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/GiniFunction.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/AttributeClassPair.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/SplitFunction.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/Splitter.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/BalancedRandomTree.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/ai/VotesCollector.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/DataCache.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/FastRfBagging.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/FastRandomForest.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/FastRfUtils.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/FastRandomTree.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/VotesCollector.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/SplitCriteria.java,> <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/hr/irb/fastRandomForest/Benchmark.java]>
using the class path: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/target/classes>:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Anisotropic_Diffusion_2D/target/Anisotropic_Diffusion_2D-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Fiji_Plugins/target/Fiji_Plugins-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/net/imagej/Image_5D/1.2.5/Image_5D-1.2.5.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Jama/target/Jama-1.0.2.jar>:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Stitching_/target/Stitching_-2.0.0-SNAPSHOT.jar>:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/VIB-lib/target/VIB-lib-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/loci/bio-formats/4.4-SNAPSHOT/bio-formats-4.4-20120306.103639-76.jar:/home/jenkins/.m2/repository/com/sun/clibwrapper_jiio/1.1/clibwrapper_jiio-1.1.jar:/home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/home/jenkins/.m2/repository/org/apache/commons/commons-math/3.0-SNAPSHOT/commons-math-3.0-20120702.214056-1.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/fiji-lib/target/fiji-lib-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/com/jgoodies/forms/1.2.1/forms-1.2.1.jar:/home/jenkins/.m2/repository/net/imagej/ij/1.46h/ij-1.46h.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/imagescience/target/imagescience-2.4.0.jar>:/home/jenkins/.m2/repository/mpicbg/imglib/2.0.0-SNAPSHOT/imglib-2.0.0-20120809.051857-553.jar:/home/jenkins/.m2/repository/mpicbg/imglib-algorithms/2.0.0-SNAPSHOT/imglib-algorithms-2.0.0-20120809.051857-553.jar:/home/jenkins/.m2/repository/mpicbg/imglib-ij/2.0.0-SNAPSHOT/imglib-ij-2.0.0-20120809.051857-553.jar:/home/jenkins/.m2/repository/net/imglib2/imglib2/2.0.0-SNAPSHOT/imglib2-2.0.0-20120809.051857-548.jar:/home/jenkins/.m2/repository/net/imglib2/imglib2-algorithms/2.0.0-SNAPSHOT/imglib2-algorithms-2.0.0-20120809.051857-548.jar:/home/jenkins/.m2/repository/net/imglib2/imglib2-ij/2.0.0-SNAPSHOT/imglib2-ij-2.0.0-20120809.051857-545.jar:/home/jenkins/.m2/repository/java3d/j3d-core/1.5.2/j3d-core-1.5.2.jar:/home/jenkins/.m2/repository/java3d/j3d-core-utils/1.5.2/j3d-core-utils-1.5.2.jar:/home/jenkins/.m2/repository/loci/jai_imageio/4.4-SNAPSHOT/jai_imageio-4.4-20120306.103244-82.jar:/home/jenkins/.m2/repository/jama/jama/1.0.2/jama-1.0.2.jar:/home/jenkins/.m2/repository/net/sf/squirrel-sql/thirdparty-non-maven/java-cup/0.11a/java-cup-0.11a.jar:/home/jenkins/.m2/repository/com/jcraft/jsch/0.1.42/jsch-0.1.42.jar:/home/jenkins/.m2/repository/junit/junit/4.5/junit-4.5.jar:/home/jenkins/.m2/repository/com/jcraft/jzlib/1.0.7/jzlib-1.0.7.jar:/home/jenkins/.m2/repository/loci/loci-common/4.4-SNAPSHOT/loci-common-4.4-20120306.103328-82.jar:/home/jenkins/.m2/repository/loci/loci_plugins/4.4-SNAPSHOT/loci_plugins-4.4-20120806.234352-138.jar:/home/jenkins/.m2/repository/log4j/log4j/1.2.14/log4j-1.2.14.jar:/home/jenkins/.m2/repository/loci/lwf-stubs/4.4-SNAPSHOT/lwf-stubs-4.4-20120306.103508-82.jar:/home/jenkins/.m2/repository/loci/mdbtools-java/4.4-SNAPSHOT/mdbtools-java-4.4-20120306.103304-82.jar:/home/jenkins/.m2/repository/loci/metakit/4.4-SNAPSHOT/metakit-4.4-20120306.103417-82.jar:/home/jenkins/.m2/repository/edu/mines/mines-jtk/20100113/mines-jtk-20100113.jar:/home/jenkins/.m2/repository/mpicbg/mpicbg/20120621/mpicbg-20120621.jar:/home/jenkins/.m2/repository/essi-unidata/netcdf-java/4.0.41/netcdf-java-4.0.41.jar:/home/jenkins/.m2/repository/loci/ome-xml/4.4-SNAPSHOT/ome-xml-4.4-20120306.103450-82.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/pal-optimization/target/pal-optimization-2.0.0-SNAPSHOT.jar>:/home/jenkins/.m2/repository/org/pentaho/pentaho-commons/pentaho-package-manager/1.0.0/pentaho-package-manager-1.0.0.jar:/home/jenkins/.m2/repository/loci/poi-loci/4.4-SNAPSHOT/poi-loci-4.4-20120306.103359-82.jar:/home/jenkins/.m2/repository/loci/scifio/4.4-SNAPSHOT/scifio-4.4-20120316.095357-49.jar:/home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.5.10/slf4j-api-1.5.10.jar:<https://qa.nest-initiative.org/job/fiji-core/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>:/home/jenkins/.m2/repository/java3d/vecmath/1.5.2/vecmath-1.5.2.jar:/home/jenkins/.m2/repository/nz/ac/waikato/cms/weka/weka-dev/3.7.6/weka-dev-3.7.6.jar
<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/utils/Utils.java>:733: cannot find symbol
symbol : constructor ByteProcessor(int,int,byte[])
location: class ij.process.ByteProcessor
isMaxPoolLabel.addSlice( new ByteProcessor( maxPoolWidth, maxPoolHeight, labelPix));
^
<https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/utils/Utils.java>:796: cannot find symbol
symbol : constructor ByteProcessor(int,int,byte[])
location: class ij.process.ByteProcessor
isMaxPoolLabel.addSlice( new ByteProcessor( width, height, labelPix));
^
Note: <https://qa.nest-initiative.org/job/fiji-core/ws/src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/Weka_Segmentation.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
2 errors
fiji.build.minimaven.JavaCompiler$CompileError: Compile error: 1
at fiji.build.minimaven.JavaCompiler.call(JavaCompiler.java:37)
at fiji.build.minimaven.POM.build(POM.java:223)
at fiji.build.minimaven.POM.buildJar(POM.java:164)
at fiji.build.SubFake.action(SubFake.java:184)
at fiji.build.Rule.make(Rule.java:195)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Rule.makePrerequisites(Rule.java:333)
at fiji.build.Rule.make(Rule.java:189)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Fake.make(Fake.java:242)
at fiji.build.Fake.main(Fake.java:56)
Compile error: 1
in rule (fiji.build.SubFake) plugins/Trainable_Segmentation.jar <...
in rule (fiji.build.All) all <- ImageJ fiji jars/VectorString.jar...
Build step 'Execute shell' marked build as failure
Archiving artifacts
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