[ImageJ-builds] Build failed in Jenkins: fiji-full #419

[Jenkins Daemon]

See <https://qa.nest-initiative.org/job/fiji-full/419/changes>

Changes:

[johannes.schindelin] Get rid of a lot of precompiled stuff

[johannes.schindelin] Clean up Fakefile

[johannes.schindelin] MiniMaven: heed the onlyNewer parameter of copyDependencies

[johannes.schindelin] Fiji Build (MiniMaven): make sure that IJ1 plugins are put into plugins/

[johannes.schindelin] Update .gitignore after recent cleanups

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Note: Recompile with -Xlint:unchecked for details.
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using the class path: <https://qa.nest-initiative.org/job/fiji-full/ws/modules/commons-math/target/classes>
Note: Some input files use or override 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.
Compiling 57 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Simple_Neurite_Tracer>
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using the class path: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Simple_Neurite_Tracer/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Viewer/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/AnalyzeSkeleton_/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Jama/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Skeletonize3D_/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/VIB-lib/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/VIB_/target/classes>:/home/jenkins/.m2/repository/batik/batik/1.8/batik-1.8.jar:<https://qa.nest-initiative.org/job/fiji-full/ws/modules/commons-math/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/fiji-lib/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib1/core/target/classes>:/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/jfree/jcommon/1.0.15/jcommon-1.0.15.jar:/home/jenkins/.m2/repository/jfree/jcommon/1.0.16/jcommon-1.0.16.jar:/home/jenkins/.m2/repository/jfree/jfreechart/1.0.13/jfreechart-1.0.13.jar:/home/jenkins/.m2/repository/junit/junit/4.5/junit-4.5.jar:/home/jenkins/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar:/home/jenkins/.m2/repository/com/jcraft/jzlib/1.0.7/jzlib-1.0.7.jar:<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/pal-optimization/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/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
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
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/3D_Viewer.jar <- src-plugins...
Parsing src-plugins/3D_Viewer/pom.xml
Checking prerequisites of (fiji.build.SubFake) jars/VIB-lib.jar <- src-plugins/VIB-...
Parsing src-plugins/VIB-lib/pom.xml
Checking prerequisites of (fiji.build.SubFake) plugins/VIB_.jar <- src-plugins/VIB_/
Parsing src-plugins/VIB_/pom.xml
Checking prerequisites of (fiji.build.SubFake) plugins/level_sets.jar <- src-plugin...
Building (fiji.build.SubFake) plugins/level_sets.jar <- src-plugin...
Parsing src-plugins/level_sets/pom.xml
Compiling 35 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets>
[-source, 1.5, -target, 1.5, -classpath, <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar,> -d, <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/target/classes,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/MorphologicalOperator.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/Filter.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/GreyScaleFilter.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/SimpleEdgeDetect.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/Canny.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/UnsetPixel.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/SUSAN.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/GreyValueErosion.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/Dilatation.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/ConvolutionFilter.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/Erosion.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/BufferedImageBuilder.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/MedianFilter.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/filter/Sobel.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/ij/ImageProgressContainer.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/ij/StateContainer.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/ij/ImageContainer.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/ij/LevelSet.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/LevelSetFactory.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/SparseFieldLevelSet.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/Coordinate.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/StagedAlgorithm.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/ActiveContours.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/DeferredObjectArray3D.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/DeferredByteArray3D.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/BandElementCache.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/BandElement.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/DeferredArray3D.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/DeferredIntArray3D.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/FastMarchingBandElement.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/FastMarching.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/DenseFieldLevelSet.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/LevelSetImplementation.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/GeodesicActiveContour.java,> <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/src/main/java/levelsets/algorithm/DeferredDoubleArray3D.java]>
using the class path: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets/target/classes>:/home/jenkins/.m2/repository/com/apple/AppleJavaExtensions/1.5/AppleJavaExtensions-1.5.jar:<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/target/classes>:<https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar>
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Checking prerequisites of (fiji.build.SubFake) jars/VectorString.jar <- jars/ij.jar...
Building (fiji.build.SubFake) jars/VectorString.jar <- jars/ij.jar...
Building in modules/TrakEM2/
Checking prerequisites of (fiji.build.CompileJar) VectorString.jar <- ini/trakem2/v...
VectorString.jar is not up-to-date because of jars/ij.jar
Building (fiji.build.CompileJar) VectorString.jar <- ini/trakem2/v...
Compiling .java files: javac -encoding UTF8 -d <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString> -source 1.5 -target 1.5 -classpath jars/ij.jar:jars/Jama.jar:java/linux/jdk1.6.0_24/jre/lib/ext/j3dcore.jar:java/linux/jdk1.6.0_24/jre/lib/ext/j3dutils.jar:java/linux/jdk1.6.0_24/jre/lib/ext/vecmath.jar -Djava.ext.dirs=<https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/lib/ext>:/usr/java/packages/lib/ext ./modules/TrakEM2/ini/trakem2/vector/SkinMaker.java ./modules/TrakEM2/ini/trakem2/vector/Util.java ./modules/TrakEM2/ini/trakem2/vector/VectorString2D.java ./modules/TrakEM2/ini/trakem2/vector/VectorString3D.java ./modules/TrakEM2/ini/trakem2/vector/VectorString.java ./modules/TrakEM2/ini/trakem2/vector/Editions.java
Making ./modules/TrakEM2/VectorString.jar from <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/Editions$1.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/Editions$Chunk.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/Editions$MinDist.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/Editions.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/SkinMaker$Match.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/SkinMaker.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/Util.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/VectorString.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/VectorString2D.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/VectorString3D$ResamplingData.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/VectorString3D$Vector.class> <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/VectorString/ini/trakem2/vector/VectorString3D.class>
Leaving modules/TrakEM2/
TrakEM2_.jar is not up-to-date because of jars/ij.jar
Building (fiji.build.SubFake) plugins/TrakEM2_.jar <- jars/ij.jar ...
Building in modules/TrakEM2/
Checking prerequisites of (fiji.build.CompileJar) TrakEM2_.jar <- ini/trakem2/imagi...
TrakEM2_.jar is not up-to-date because of jars/ij.jar
Building (fiji.build.CompileJar) TrakEM2_.jar <- ini/trakem2/imagi...
Compiling .java files: javac -encoding UTF8 -d <https://qa.nest-initiative.org/job/fiji-full/ws/./modules/TrakEM2/build/TrakEM2_> -source 1.5 -target 1.5 -classpath jars/ij.jar:jars/jai_core.jar:jars/jai_codec.jar:jars/VectorString.jar:jars/postgresql.jar:jars/jcommon.jar:jars/jfreechart.jar:jars/edu_mines_jtk.jar:jars/VIB-lib.jar:plugins/VIB_.jar:jars/mpicbg.jar:plugins/loci_tools.jar:plugins/bUnwarpJ_.jar:plugins/level_sets.jar:plugins/Fiji_Plugins.jar:jars/Jama.jar:jars/imglib.jar:jars/imglib-algorithms.jar:jars/imglib-ij.jar:plugins/Simple_Neurite_Tracer.jar:plugins/3D_Viewer.jar:plugins/Lasso_and_Blow_Tool.jar:plugins/mpicbg_.jar:java/linux/jdk1.6.0_24/jre/lib/ext/j3dcore.jar:java/linux/jdk1.6.0_24/jre/lib/ext/j3dutils.jar:java/linux/jdk1.6.0_24/jre/lib/ext/vecmath.jar -Djava.ext.dirs=<https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/lib/ext>:/usr/java/packages/lib/ext ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTRed.java ./modules/TrakEM2/mpicbg/trakem2/transform/TranslationModel2D.java ./modules/TrakEM2/ini/trakem2/display/Region.java ./modules/TrakEM2/ini/trakem2/display/NonLinearTransformMode.java ./modules/TrakEM2/ini/trakem2/display/Mode.java ./modules/TrakEM2/ini/trakem2/imaging/BinaryInterpolation2D.java ./modules/TrakEM2/ini/trakem2/display/inspect/ShapeProxy.java ./modules/TrakEM2/ini/trakem2/analysis/Vertex.java ./modules/TrakEM2/ini/trakem2/utils/TaskOnEDT.java ./modules/TrakEM2/ini/trakem2/display/AffineTransformMode.java ./modules/TrakEM2/bunwarpj/trakem2/transform/CubicBSplineTransform.java ./modules/TrakEM2/ini/trakem2/imaging/ImagePreprocessor.java ./modules/TrakEM2/ini/trakem2/display/Overlay.java ./modules/TrakEM2/ini/trakem2/display/AreaContainer.java ./modules/TrakEM2/ini/trakem2/imaging/LayerStack.java ./modules/TrakEM2/ini/trakem2/persistence/StaleFiles.java ./modules/TrakEM2/ini/trakem2/display/DLabel.java ./modules/TrakEM2/mpi/fruitfly/math/Quicksortable.java ./modules/TrakEM2/ini/trakem2/display/Stack.java ./modules/TrakEM2/ini/trakem2/persistence/TMLHandler.java ./modules/TrakEM2/ini/trakem2/display/Selection.java ./modules/TrakEM2/ini/trakem2/display/Displayable.java ./modules/TrakEM2/ini/trakem2/tree/DNDTree.java ./modules/TrakEM2/ini/trakem2/persistence/DownsamplerMipMaps.java ./modules/TrakEM2/ini/trakem2/persistence/ProjectTiler.java ./modules/TrakEM2/ini/trakem2/display/graphics/MultiplyARGBComposite.java ./modules/TrakEM2/ini/trakem2/display/VectorData.java ./modules/TrakEM2/ini/trakem2/utils/StopWatch.java ./modules/TrakEM2/ini/trakem2/utils/FieldMapView.java ./modules/TrakEM2/ini/trakem2/imaging/Blending.java ./modules/TrakEM2/ini/trakem2/display/Bucket.java ./modules/TrakEM2/ini/trakem2/utils/ReconstructArea.java ./modules/TrakEM2/ini/trakem2/persistence/FSLoader.java ./modules/TrakEM2/ini/trakem2/imaging/LazyVirtualStack.java ./modules/TrakEM2/mpi/fruitfly/math/datastructures/FloatArray2D.java ./modules/TrakEM2/ini/trakem2/tree/TrakEM2MLParser.java ./modules/TrakEM2/ini/trakem2/tree/ProjectThing.java ./modules/TrakEM2/ini/trakem2/display/MipMapImage.java ./modules/TrakEM2/mpicbg/trakem2/align/GenericAffineTile2D.java ./modules/TrakEM2/ini/trakem2/io/ImageFileFilter.java ./modules/TrakEM2/ini/trakem2/imaging/FloatProcessorT2.java ./modules/TrakEM2/ini/trakem2/display/RollingPanel.java ./modules/TrakEM2/ini/trakem2/New_Project.java ./modules/TrakEM2/ini/trakem2/tree/RenameThingStep.java ./modules/TrakEM2/ini/trakem2/io/CoordinateTransformXML.java ./modules/TrakEM2/ini/trakem2/utils/OptionPanel.java ./modules/TrakEM2/ini/trakem2/persistence/Loader.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTCyan.java ./modules/TrakEM2/ini/trakem2/display/Bucketable.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTBlue.java ./modules/TrakEM2/ini/trakem2/utils/TypedHashMap.java ./modules/TrakEM2/ini/trakem2/display/VectorDataTransform.java ./modules/TrakEM2/mpicbg/trakem2/align/AffineTile2D.java ./modules/TrakEM2/ini/trakem2/io/ImageSaver.java ./modules/TrakEM2/ini/trakem2/imaging/FastIntegralImage.java ./modules/TrakEM2/ini/trakem2/display/graphics/DifferenceARGBComposite.java ./modules/TrakEM2/mpi/fruitfly/registration/ImageFilter.java ./modules/TrakEM2/ini/trakem2/analysis/Centrality.java ./modules/TrakEM2/ini/trakem2/display/Paintable.java ./modules/TrakEM2/ini/trakem2/display/AreaTree.java ./modules/TrakEM2/ini/trakem2/imaging/filters/GaussianBlur.java ./modules/TrakEM2/ini/trakem2/display/Layer.java ./modules/TrakEM2/ini/trakem2/display/GroupingMode.java ./modules/TrakEM2/ini/trakem2/display/AreaWrapper.java ./modules/TrakEM2/ini/trakem2/utils/StdOutWindow.java ./modules/TrakEM2/ini/trakem2/display/Line3D.java ./modules/TrakEM2/ini/trakem2/io/RawMipMaps.java ./modules/TrakEM2/mpicbg/trakem2/transform/ExportedTile.java ./modules/TrakEM2/ini/trakem2/tree/TransferableNode.java ./modules/TrakEM2/ini/trakem2/imaging/Segmentation.java ./modules/TrakEM2/ini/trakem2/parallel/TaskFactory.java ./modules/TrakEM2/ini/trakem2/display/Dissector.java ./modules/TrakEM2/ini/trakem2/display/ManualAlignMode.java ./modules/TrakEM2/mpicbg/trakem2/transform/TranslationModel3D.java ./modules/TrakEM2/ini/trakem2/io/ImageFileHeader.java ./modules/TrakEM2/ini/trakem2/imaging/ContrastPlot.java ./modules/TrakEM2/ini/trakem2/display/Treeline.java ./modules/TrakEM2/ini/trakem2/display/Pipe.java ./modules/TrakEM2/ini/trakem2/tree/TemplateThing.java ./modules/TrakEM2/ini/trakem2/display/TreeConnectorsView.java ./modules/TrakEM2/ini/trakem2/utils/Saver.java ./modules/TrakEM2/ini/trakem2/display/FakeImagePlus.java ./modules/TrakEM2/ini/trakem2/display/AbstractRepaintThread.java ./modules/TrakEM2/mpicbg/trakem2/transform/TransformMeshMappingWithMasks.java ./modules/TrakEM2/ini/trakem2/scripting/PatchScript.java ./modules/TrakEM2/ini/trakem2/analysis/Compare.java ./modules/TrakEM2/ini/trakem2/tree/ProjectTree.java ./modules/TrakEM2/ini/trakem2/display/ImageData.java ./modules/TrakEM2/ini/trakem2/utils/M.java ./modules/TrakEM2/ini/trakem2/imaging/filters/SubtractBackground.java ./modules/TrakEM2/mpi/fruitfly/general/MultiThreading.java ./modules/TrakEM2/ini/trakem2/display/LayerSet.java ./modules/TrakEM2/ini/trakem2/display/FakeImageWindow.java ./modules/TrakEM2/ini/trakem2/display/DisplayableChooser.java ./modules/TrakEM2/ini/trakem2/imaging/filters/NormalizeLocalContrast.java ./modules/TrakEM2/mpicbg/trakem2/align/Align.java ./modules/TrakEM2/ini/trakem2/display/DisplayCanvas.java ./modules/TrakEM2/ini/trakem2/imaging/P.java ./modules/TrakEM2/ini/trakem2/display/d3d/ControlClickBehavior.java ./modules/TrakEM2/ini/trakem2/utils/IJError.java ./modules/TrakEM2/ini/trakem2/tree/AbstractTreeTransferHandler.java ./modules/TrakEM2/mpicbg/trakem2/transform/InvertibleCoordinateTransform.java ./modules/TrakEM2/mpicbg/trakem2/align/SimilarityTile2D.java ./modules/TrakEM2/mpicbg/trakem2/transform/AffineModel2D.java ./modules/TrakEM2/ini/trakem2/display/Node.java ./modules/TrakEM2/ini/trakem2/display/DisplayablePanel.java ./modules/TrakEM2/ini/trakem2/display/Tree.java ./modules/TrakEM2/ini/trakem2/imaging/filters/RankFilter.java ./modules/TrakEM2/ini/trakem2/display/LayerPanel.java ./modules/TrakEM2/ini/trakem2/display/Ball.java ./modules/TrakEM2/mpicbg/trakem2/transform/DTD.java ./modules/TrakEM2/ini/trakem2/utils/Search.java ./modules/TrakEM2/ini/trakem2/display/graphics/SubtractARGBComposite.java ./modules/TrakEM2/ini/trakem2/tree/LayerThing.java ./modules/TrakEM2/ini/trakem2/tree/DTDParser.java ./modules/TrakEM2/ini/trakem2/utils/ProjectToolbar.java ./modules/TrakEM2/ini/trakem2/display/graphics/ColorYCbCrComposite.java ./modules/TrakEM2/mpicbg/trakem2/align/Util.java ./modules/TrakEM2/ini/trakem2/display/inspect/InspectPatchTrianglesMode.java ./modules/TrakEM2/mpicbg/trakem2/align/RegularizedAffineLayerAlignment.java ./modules/TrakEM2/ini/trakem2/display/SnapshotPanel.java ./modules/TrakEM2/ini/trakem2/utils/Filter.java ./modules/TrakEM2/ini/trakem2/imaging/filters/EqualizeHistogram.java ./modules/TrakEM2/ini/trakem2/imaging/filters/EnhanceContrast.java ./modules/TrakEM2/ini/trakem2/display/Taggable.java ./modules/TrakEM2/ini/trakem2/utils/Dispatcher.java ./modules/TrakEM2/ini/trakem2/io/AmiraImporter.java ./modules/TrakEM2/ini/trakem2/display/Channel.java ./modules/TrakEM2/ini/trakem2/utils/AreaUtils.java ./modules/TrakEM2/ini/trakem2/display/paint/USHORTPaint.java ./modules/TrakEM2/ini/trakem2/parallel/Process.java ./modules/TrakEM2/ini/trakem2/imaging/filters/IFilter.java ./modules/TrakEM2/ini/trakem2/utils/DNDInsertImage.java ./modules/TrakEM2/mpicbg/trakem2/util/Triple.java ./modules/TrakEM2/mpi/fruitfly/math/datastructures/FloatArray4D.java ./modules/TrakEM2/ini/trakem2/display/Display.java ./modules/TrakEM2/ini/trakem2/utils/Montage.java ./modules/TrakEM2/ini/trakem2/imaging/filters/DefaultMinAndMax.java ./modules/TrakEM2/mpicbg/trakem2/transform/CoordinateTransform.java ./modules/TrakEM2/ini/trakem2/utils/IntegerField.java ./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java ./modules/TrakEM2/ini/trakem2/utils/Utils.java ./modules/TrakEM2/ini/trakem2/utils/BigBrother.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTMagenta.java ./modules/TrakEM2/mpicbg/trakem2/transform/ExportUnsignedShort.java ./modules/TrakEM2/mpicbg/trakem2/align/AbstractAffineTile2D.java ./modules/TrakEM2/mpicbg/trakem2/transform/MovingLeastSquaresTransform2.java ./modules/TrakEM2/ini/trakem2/utils/Worker.java ./modules/TrakEM2/mpicbg/trakem2/align/AlignLayersTask.java ./modules/TrakEM2/ini/trakem2/Open_DB_Project.java ./modules/TrakEM2/ini/trakem2/imaging/ContrastEnhancerWrapper.java ./modules/TrakEM2/ini/trakem2/io/LoggingInputStream.java ./modules/TrakEM2/ini/trakem2/persistence/Cache.java ./modules/TrakEM2/ini/trakem2/io/XMLFileFilter.java ./modules/TrakEM2/lenscorrection/DistortionCorrectionTask.java ./modules/TrakEM2/ini/trakem2/display/YesNoDialog.java ./modules/TrakEM2/ini/trakem2/display/graphics/GraphicsSource.java ./modules/TrakEM2/mpicbg/trakem2/align/ElasticLayerAlignment.java ./modules/TrakEM2/ini/trakem2/display/graphics/DefaultGraphicsSource.java ./modules/TrakEM2/ini/trakem2/display/Display3D.java ./modules/TrakEM2/ini/trakem2/display/d3d/Display3DGUI.java ./modules/TrakEM2/ini/trakem2/New_DB_Project.java ./modules/TrakEM2/mpicbg/trakem2/transform/SimilarityModel2D.java ./modules/TrakEM2/ini/trakem2/persistence/XMLOptions.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTCustom.java ./modules/TrakEM2/ini/trakem2/display/AreaList.java ./modules/TrakEM2/mpicbg/trakem2/align/AlignTask.java ./modules/TrakEM2/lenscorrection/NonLinearTransform.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTGreen.java ./modules/TrakEM2/mpicbg/trakem2/align/TranslationTile2D.java ./modules/TrakEM2/ini/trakem2/tree/LayerTree.java ./modules/TrakEM2/ini/trakem2/parallel/CountingTaskFactory.java ./modules/TrakEM2/ini/trakem2/Project.java ./modules/TrakEM2/ini/trakem2/utils/Vector3.java ./modules/TrakEM2/ini/trakem2/display/Tag.java ./modules/TrakEM2/lenscorrection/PolynomialModel2D.java ./modules/TrakEM2/mpi/fruitfly/general/ArrayConverter.java ./modules/TrakEM2/mpicbg/trakem2/transform/CoordinateTransformList.java ./modules/TrakEM2/mpicbg/trakem2/transform/AffineModel3D.java ./modules/TrakEM2/ini/trakem2/display/TransformationStep.java ./modules/TrakEM2/ini/trakem2/io/NeuroML.java ./modules/TrakEM2/ini/trakem2/display/paint/USHORTPaintContext.java ./modules/TrakEM2/ini/trakem2/utils/RedPhone.java ./modules/TrakEM2/ini/trakem2/display/Coordinate.java ./modules/TrakEM2/ini/trakem2/persistence/ImageBytes.java ./modules/TrakEM2/ini/trakem2/imaging/PatchStack.java ./modules/TrakEM2/ini/trakem2/display/ZDisplayable.java ./modules/TrakEM2/ini/trakem2/tree/Thing.java ./modules/TrakEM2/ini/trakem2/persistence/FilePathRepair.java ./modules/TrakEM2/ini/trakem2/display/AbstractOffscreenThread.java ./modules/TrakEM2/mpicbg/trakem2/align/ElasticMontage.java ./modules/TrakEM2/mpicbg/trakem2/transform/TransformMesh.java ./modules/TrakEM2/ini/trakem2/imaging/filters/CLAHE.java ./modules/TrakEM2/ini/trakem2/io/RagMipMaps.java ./modules/TrakEM2/ini/trakem2/display/graphics/TestGraphicsSource.java ./modules/TrakEM2/mpi/fruitfly/math/General.java ./modules/TrakEM2/mpi/fruitfly/general/ImageArrayConverter.java ./modules/TrakEM2/ini/trakem2/display/FreeHandProfile.java ./modules/TrakEM2/mpicbg/trakem2/align/AbstractElasticAlignment.java ./modules/TrakEM2/mpicbg/trakem2/transform/RigidModel2D.java ./modules/TrakEM2/ini/trakem2/persistence/DBObject.java ./modules/TrakEM2/mpicbg/trakem2/align/RigidTile2D.java ./modules/TrakEM2/ini/trakem2/display/Polyline.java ./modules/TrakEM2/lenscorrection/Distortion_Correction.java ./modules/TrakEM2/ini/trakem2/display/Patch.java ./modules/TrakEM2/ini/trakem2/imaging/StitchingTEM.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTYellow.java ./modules/TrakEM2/ini/trakem2/tree/TemplateTree.java ./modules/TrakEM2/ini/trakem2/imaging/filters/Normalize.java ./modules/TrakEM2/ini/trakem2/display/ImageJCommandListener.java ./modules/TrakEM2/mpi/fruitfly/math/datastructures/FloatArray3D.java ./modules/TrakEM2/ini/trakem2/display/DoStep.java ./modules/TrakEM2/mpicbg/trakem2/transform/MovingLeastSquaresTransform.java ./modules/TrakEM2/ini/trakem2/Open_Project.java ./modules/TrakEM2/ini/trakem2/imaging/filters/FilterEditor.java ./modules/TrakEM2/ini/trakem2/display/Profile.java ./modules/TrakEM2/mpicbg/trakem2/util/Downsampler.java ./modules/TrakEM2/ini/trakem2/utils/Merger.java ./modules/TrakEM2/ini/trakem2/display/DisplayNavigator.java ./modules/TrakEM2/ini/trakem2/tree/DefaultTreeTransferHandler.java ./modules/TrakEM2/ini/trakem2/ControlWindow.java ./modules/TrakEM2/mpi/fruitfly/registration/CrossCorrelation2D.java ./modules/TrakEM2/ini/trakem2/analysis/Graph.java ./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java ./modules/TrakEM2/ini/trakem2/tree/TitledThing.java ./modules/TrakEM2/ini/trakem2/utils/CachingThread.java ./modules/TrakEM2/ini/trakem2/utils/Lock.java ./modules/TrakEM2/mpicbg/trakem2/align/TileConfiguration.java ./modules/TrakEM2/ini/trakem2/display/DefaultMode.java ./modules/TrakEM2/mpi/fruitfly/math/datastructures/FloatArray.java ./modules/TrakEM2/ini/trakem2/imaging/filters/Invert.java ./modules/TrakEM2/ini/trakem2/display/ContrastAdjustmentMode.java ./modules/TrakEM2/ini/trakem2/plugin/TPlugIn.java ./modules/TrakEM2/ini/trakem2/display/graphics/AddARGBComposite.java ./modules/TrakEM2/ini/trakem2/imaging/filters/ResetMinAndMax.java ./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java ./modules/TrakEM2/ini/trakem2/utils/Render.java ./modules/TrakEM2/mpicbg/trakem2/transform/InvertibleCoordinateTransformList.java ./modules/TrakEM2/ini/trakem2/imaging/filters/LUTOrange.java ./modules/TrakEM2/ini/trakem2/display/Connector.java ./modules/TrakEM2/ini/trakem2/utils/History.java ./modules/TrakEM2/ini/trakem2/utils/Bureaucrat.java ./modules/TrakEM2/mpicbg/trakem2/transform/TransformMeshMapping.java ./modules/TrakEM2/ini/trakem2/utils/Operation.java
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:73: package javax.media.jai does not exist
import javax.media.jai.PlanarImage;
                      ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:75: package com.sun.media.jai.codec does not exist
import com.sun.media.jai.codec.ImageCodec;
                              ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:76: package com.sun.media.jai.codec does not exist
import com.sun.media.jai.codec.TIFFDecodeParam;
                              ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:77: package com.sun.media.jai.codec does not exist
import com.sun.media.jai.codec.TIFFEncodeParam;
                              ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:96: package org.postgresql.geometric does not exist
import org.postgresql.geometric.PGpoint;
                               ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:97: package org.postgresql.geometric does not exist
import org.postgresql.geometric.PGpolygon;
                               ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:98: package org.postgresql does not exist
import org.postgresql.*;
^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:99: package org.postgresql.core does not exist
import org.postgresql.core.PGStream;
                          ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:100: package org.postgresql.core.v3 does not exist
import org.postgresql.core.v3.*;
^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:101: package org.postgresql.jdbc2 does not exist
import org.postgresql.jdbc2.*;
^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:102: package org.postgresql.jdbc3 does not exist
import org.postgresql.jdbc3.*;
^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1232: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
	private double[][][] toBezierArrays(final PGpolygon polygon) {
	                                          ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1975: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
	private PGpolygon makePGpolygon(final double[][][] bezarr) {
	        ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1988: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
	private Polygon makePolygon(PGpolygon pg) {
	                            ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2382: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
	private PGpolygon makePGpolygon(final ArrayList al_points) {
	        ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:773: cannot find symbol
symbol  : class TIFFEncodeParam
location: class ini.trakem2.io.ImageSaver
				final TIFFEncodeParam param = new TIFFEncodeParam();
				      ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:773: cannot find symbol
symbol  : class TIFFEncodeParam
location: class ini.trakem2.io.ImageSaver
				final TIFFEncodeParam param = new TIFFEncodeParam();
				                                  ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:775: cannot find symbol
symbol  : variable TIFFEncodeParam
location: class ini.trakem2.io.ImageSaver
				param.setCompression(TIFFEncodeParam.COMPRESSION_NONE);
				                     ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:777: cannot find symbol
symbol  : variable ImageCodec
location: class ini.trakem2.io.ImageSaver
				ImageCodec.createImageEncoder("TIFF", out, param).encode(bi);
				^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:801: cannot find symbol
symbol  : class TIFFDecodeParam
location: class ini.trakem2.io.ImageSaver
		return PlanarImage.wrapRenderedImage(ImageCodec.createImageDecoder("TIFF", new File(path), new TIFFDecodeParam()).decodeAsRenderedImage()).getAsBufferedImage();
		                                                                                               ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:801: cannot find symbol
symbol  : variable ImageCodec
location: class ini.trakem2.io.ImageSaver
		return PlanarImage.wrapRenderedImage(ImageCodec.createImageDecoder("TIFF", new File(path), new TIFFDecodeParam()).decodeAsRenderedImage()).getAsBufferedImage();
		                                     ^
./modules/TrakEM2/ini/trakem2/io/ImageSaver.java:801: cannot find symbol
symbol  : variable PlanarImage
location: class ini.trakem2.io.ImageSaver
		return PlanarImage.wrapRenderedImage(ImageCodec.createImageDecoder("TIFF", new File(path), new TIFFDecodeParam()).decodeAsRenderedImage()).getAsBufferedImage();
		       ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:156: cannot find symbol
symbol  : class Driver
location: class ini.trakem2.persistence.DBLoader
					Utils.log("Loader: could not load "+Driver.class.getName()+": " + cnfe);
					                                    ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1215: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
			PGpolygon p = null;
			^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1219: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
					p = (PGpolygon)r.getObject("polygon");
					     ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1267: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
				PGpolygon pol = (PGpolygon)r.getObject("polygon");
				^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1267: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
				PGpolygon pol = (PGpolygon)r.getObject("polygon");
				                 ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1976: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
		final PGpoint[] points = new PGpoint[bezarr[0][0].length * 3];
		      ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1976: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
		final PGpoint[] points = new PGpoint[bezarr[0][0].length * 3];
		                             ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1981: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
			points[i] = new PGpoint(p_l[0][j], p_l[1][j]);
			                ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1982: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
			points[i+1] = new PGpoint(p[0][j], p[1][j]);
			                  ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1983: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
			points[i+2] = new PGpoint(p_r[0][j], p_r[1][j]);
			                  ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:1985: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
		return new PGpolygon(points);
		           ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2383: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
		final PGpoint[] pol = new PGpoint[al_points.size()];
		      ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2383: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
		final PGpoint[] pol = new PGpoint[al_points.size()];
		                          ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2386: cannot find symbol
symbol  : class PGpoint
location: class ini.trakem2.persistence.DBLoader
			pol[i] = new PGpoint(p.x, p.y);
			             ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2388: cannot find symbol
symbol  : class PGpolygon
location: class ini.trakem2.persistence.DBLoader
		return new PGpolygon(pol);
		           ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2628: cannot find symbol
symbol  : class AbstractJdbc2Connection
location: class ini.trakem2.persistence.DBLoader.Monitor
				AbstractJdbc2Connection a2 = (AbstractJdbc2Connection)connection;
				^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2628: cannot find symbol
symbol  : class AbstractJdbc2Connection
location: class ini.trakem2.persistence.DBLoader.Monitor
				AbstractJdbc2Connection a2 = (AbstractJdbc2Connection)connection;
				                              ^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2638: cannot find symbol
symbol  : class PGStream
location: class ini.trakem2.persistence.DBLoader.Monitor
				PGStream pgstream = (PGStream)f_pgstream.get(pci);
				^
./modules/TrakEM2/ini/trakem2/persistence/DBLoader.java:2638: cannot find symbol
symbol  : class PGStream
location: class ini.trakem2.persistence.DBLoader.Monitor
				PGStream pgstream = (PGStream)f_pgstream.get(pci);
				                     ^
Note: Some input files use or override 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.
41 errors
Fake failed: Compile error: 1
	in rule (fiji.build.CompileJar) TrakEM2_.jar <- ini/trakem2/imagi...
	in rule (fiji.build.SubFake) plugins/TrakEM2_.jar <- jars/ij.jar ...
	in rule (fiji.build.All) all <- ImageJ fiji jars/VectorString.jar...
Build step 'Execute shell' marked build as failure
Archiving artifacts