[ImageJ-bugs] [Bug 1210] New: trakem: import stack fails to complete

bugzilla at fiji.sc bugzilla at fiji.sc
Tue Dec 29 04:28:58 CST 2015 

http://fiji.sc/bugzilla/show_bug.cgi?id=1210

            Bug ID: 1210
           Summary: trakem: import stack fails to complete
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: felix.meyenhofer at unifr.ch
                CC: felix.meyenhofer at unifr.ch

When importing a stack (drag and drop into a blank project)

the following error occurs:

[ERROR] Uncaught exception in thread Thread[T2-Canvas-Offscreen,5,main]
java.lang.NoClassDefFoundError: javax/vecmath/Tuple3d
    at ini.trakem2.display.Bucket.find(Bucket.java:211)
~[TrakEM2_-1.0g.jar:1.0g]
    at ini.trakem2.display.Bucket.find(Bucket.java:194)
~[TrakEM2_-1.0g.jar:1.0g]
    at ini.trakem2.display.Layer.find(Layer.java:657) ~[TrakEM2_-1.0g.jar:1.0g]
    at
ini.trakem2.display.DisplayCanvas.gatherDisplayables(DisplayCanvas.java:2482)
~[TrakEM2_-1.0g.jar:1.0g]
    at
ini.trakem2.display.DisplayCanvas.paintOffscreen(DisplayCanvas.java:2577)
~[TrakEM2_-1.0g.jar:1.0g]
    at
ini.trakem2.display.DisplayCanvas$OffscreenThread.paint(DisplayCanvas.java:2452)
~[TrakEM2_-1.0g.jar:1.0g]
    at
ini.trakem2.display.AbstractOffscreenThread.run(AbstractOffscreenThread.java:55)
~[TrakEM2_-1.0g.jar:1.0g]
Caused by: java.lang.ClassNotFoundException: javax.vecmath.Tuple3d
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
~[na:1.8.0_66]
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[na:1.8.0_66]
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
~[na:1.8.0_66]
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_66]
    ... 7 common frames omitted
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plugins/Examples/TrakEM2_Example_Scripts/extract_stack_under_arealist.py
done
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scripts/IsJava3DInstalled.m done
scripts/Matlab3DViewerDemo_1.m done
scripts/Matlab3DViewerDemo_2.m done
scripts/Matlab3DViewerDemo_3.m done
scripts/Matlab3DViewerIntroduction.m done
scripts/Miji.m done
scripts/Miji_Test.m done
macros/AutoRun/AutoRun_Scripts.ijm done
macros/listManagement.txt done
macros/StartupMacros.fiji.ijm done
macros/toolsets/Clear Custom Tools.txt done
macros/toolsets/Drawing Tools.txt done
macros/toolsets/Lookup Tables.txt done
luts/16_colors.lut done
luts/5_ramps.lut done
Checksummer 211877878/221226163
luts/6_shades.lut done
luts/blue_orange_icb.lut done
luts/brgbcmyw.lut done
luts/cool.lut done
luts/Cyan Hot.lut done
luts/edges.lut done
luts/gem.lut done
luts/glasbey.lut done
luts/glow.lut done
luts/Green Fire Blue.lut done
luts/HiLo.lut done
luts/ICA.lut done
luts/ICA2.lut done
luts/ICA3.lut done
luts/Magenta Hot.lut done
luts/Orange Hot.lut done
luts/phase.lut done
luts/physics.lut done
luts/Rainbow RGB.lut done
luts/Red Hot.lut done
luts/royal.lut done
luts/sepia.lut done
luts/smart.lut done
luts/thal.lut done
luts/thallium.lut done
luts/Thermal.lut done
luts/unionjack.lut done
luts/Yellow Hot.lut done
images/about/about1.tif done
images/about/about1.tif.txt done
images/about/about2.tif done
images/about/about2.tif.txt done
images/about/about3.tif done
images/about/about3.tif.txt done
images/about/about4.tif done
images/about/about4.tif.txt done
images/about/about5.tif done
images/about/about5.tif.txt done
images/icon-flat.png done
images/icon.png done
Contents/Info.plist done
Contents/Resources/Fiji.icns done
Contents/Resources/ImageJ.icns done
jars/jai_imageio-1.0.1.jar done
jars/lwf-stubs-4.4.8.jar done
jars/ij-io-2.0.0-beta-7.jar done
jars/ij-plugins-debug-2.0.0-SNAPSHOT.jar done
jars/ij-updater-core-2.0.0-beta-7.7.jar done
jars/ij-plugins-data-2.0.0-SNAPSHOT.jar done
jars/ij-plugins-display-2.0.0-SNAPSHOT.jar done
jars/ij-ui-swing-tools-2.0.0-beta-7.7.jar done
jars/ij-ui-swing-sdi-2.0.0-SNAPSHOT.jar done
jars/xalan-2.7.1.jar done
jars/ij-updater-ssh-2.0.0-beta-7.7.jar done
jars/ij-ui-swing-updater-2.0.0-beta-7.7.jar done
jars/ij-ext-swing-2.0.0-SNAPSHOT.jar done
jars/ij-ui-common-awt-2.0.0-beta-7.7.jar done
jars/ome-xml-4.4.10.jar done
jars/ij-platform-2.0.0-SNAPSHOT.jar done
jars/ij-plugins-misc-2.0.0-SNAPSHOT.jar done
jars/ij-util-awt-2.0.0-beta-7.7.jar done
jars/ij-core-2.0.0-beta-7.7.jar done
jars/ij-platform-macosx-2.0.0-SNAPSHOT.jar done
jars/ij-tools-2.0.0-beta-7.7.jar done
jars/sezpoz-1.9-imagej.jar done
jars/serializer-2.7.1.jar done
jars/ij-ui-2.0.0-beta-7.7.jar done
jars/imglib2-ops-2.0.0-beta-26.jar done
jars/ij-ui-swing-base-2.0.0-SNAPSHOT.jar done
jars/ij-legacy-2.0.0-SNAPSHOT.jar done
jars/ij-data-2.0.0-beta-7.7.jar done
jars/slf4j-log4j12-1.7.2.jar done
jars/ij-plugins-app-2.0.0-SNAPSHOT.jar done
jars/ij-ui-swing-plugins-2.0.0-beta5.jar done
jars/loci-common-4.4.10.jar done
jars/ij-options-2.0.0-beta-7.7.jar done
jars/forms-1.3.0.jar done
jars/ij-app-2.0.0-beta-7.7.jar done
jars/ij-util-swing-2.0.0-beta-7.7.jar done
jars/imglib2-algorithms-2.0.0-beta-26.jar done
jars/imglib2-io-2.0.0-beta-20.jar done
jars/clibwrapper_jiio.jar done
Contents/MacOS/ImageJ-macosx done
Contents/MacOS/ImageJ-tiger done
ImageJ-linux32 done
ImageJ-linux64 done
ImageJ-win32.exe done
jars/ij-launcher.jar done
jars/ij-platforms-2.0.0-beta-7.7.jar done
jars/ij-commands-app-2.0.0-SNAPSHOT.jar done
jars/ij-commands-data-2.0.0-SNAPSHOT.jar done
jars/ij-commands-debug-2.0.0-SNAPSHOT.jar done
jars/ij-commands-display-2.0.0-SNAPSHOT.jar done
jars/ij-commands-misc-2.0.0-SNAPSHOT.jar done
jars/ij-ui-swing-2.0.0-beta-7.7.jar done
jars/ij-ui-swing-script-editor-2.0.0-beta-7.7.jar done
jars/ij-minimaven-2.0.0-beta-7.7.jar done
jars/ij-script-beanshell-2.0.0-SNAPSHOT.jar done
jars/ij-script-java-2.0.0-SNAPSHOT.jar done
jars/ij-ui-swing-commands-2.0.0-beta-7.7.jar done
jars/loci-legacy-4.5-SNAPSHOT.jar done
jars/scifio-devel-4.5-SNAPSHOT.jar done
jars/ij-scripting-beanshell-2.0.0-beta-7.7.jar done
jars/turbojpeg-4.5-SNAPSHOT.jar done
jars/ij-scripting-java-2.0.0-beta-7.7.jar done
jars/ij-commands-2.0.0-beta-7.7.jar done
jars/ij-updater-webdav-2.0.0-beta-7.7.jar done
jars/kryo-2.21-shaded.jar done
jars/ij-text-2.0.0-beta-7.7.jar done
jars/imglib2-meta-2.0.0-beta-26.jar done
jars/ij-scripting-clojure-2.0.0-beta-7.7.jar done
jars/ij-scripting-jruby-2.0.0-beta-7.7.jar done
jars/ij-scripting-jython-2.0.0-beta-7.7.jar done
jars/jruby.jar done
jars/jython.jar done
jars/ij-scripting-javascript-2.0.0-beta-7.7.jar done
jars/jruby-complete-1.7.11.jar done
jars/junit-4.8.1.jar done
jars/hamcrest-core-1.3.jar done
jars/imagej-usage-0.2.0.jar done
jars/json-20140107.jar done
jars/jython-standalone-2.5.3.jar done
jars/edu_mines_jtk.jar done
jars/imglib2-algorithms-gpl-2.0.0-beta-26.jar done
jars/imglib2-algorithms-legacy-2.0.0-beta-26.jar done
jars/jai_codec.jar done
jars/jai_core.jar done
jars/Jama.jar done
jars/jdom-2.0.2.jar done
jars/jdom-contrib.jar done
plugins/Script_Editor-2.0.0-SNAPSHOT.jar done
plugins/Threshold_Colour-2.0.1.jar done
jars/netcdf-java-4.0.03.jar done
jars/metakit-4.4.10.jar done
jars/imglib-scripting.jar done
jars/imglib-io-2.0.0-SNAPSHOT.jar done
jars/poi-loci-4.4.10.jar done
jars/imglib-algorithms-2.0.0-SNAPSHOT.jar done
jars/imglib.jar done
jars/weka.jar done
jars/commons-math.jar done
jars/imglib-ij.jar done
jars/bio-formats-4.4.10.jar done
jars/mdbtools-java-4.4.10.jar done
plugins/loci_plugins-4.4.10.jar done
plugins/Daltonize_.jar done
plugins/Record_Screen.jar done
plugins/loci_tools.jar done
jars/jgrapht-jdk1.6.jar done
fiji-linux done
fiji-linux64 done
fiji-win32.exe done
fiji-win64.exe done
Contents/MacOS/fiji-macosx done
Contents/MacOS/fiji-tiger done
jars/bio-formats/scifio-4.4.10.jar done
jars/ome-formats-0.6.1.jar done
jars/bio-formats/formats-gpl.5.0.0.jar done
jars/ffmpeg-2.6.1-0.11-linux-x86_64.jar done
jars/ffmpeg-2.6.1-0.11-macosx-x86_64.jar done
jars/ffmpeg-2.6.1-0.11-windows-x86.jar done
jars/ffmpeg-2.6.1-0.11-windows-x86_64.jar done
jars/ffmpeg-2.6.1-0.11-android-arm.jar done
jars/ffmpeg-2.6.1-0.11-android-x86.jar done
jars/ffmpeg-2.6.1-0.11-linux-x86.jar done
jars/linux32/ffmpeg-2.6.1-0.11-linux-x86.jar done
jars/linux64/ffmpeg-2.6.1-0.11-linux-x86_64.jar done
jars/macosx/ffmpeg-2.6.1-0.11-macosx-x86_64.jar done
jars/win32/ffmpeg-2.6.1-0.11-windows-x86.jar done
jars/gluegen-rt-2.3.2-natives-android-aarch64.jar done
jars/gluegen-rt-2.3.2-natives-android-armv6.jar done
jars/gluegen-rt-2.3.2-natives-linux-amd64.jar done
jars/gluegen-rt-2.3.2-natives-linux-armv6.jar done
jars/gluegen-rt-2.3.2-natives-linux-armv6hf.jar done
jars/gluegen-rt-2.3.2-natives-linux-i586.jar done
jars/gluegen-rt-2.3.2-natives-macosx-universal.jar done
jars/gluegen-rt-2.3.2-natives-solaris-amd64.jar done
jars/gluegen-rt-2.3.2-natives-solaris-i586.jar done
jars/gluegen-rt-2.3.2-natives-windows-amd64.jar done
jars/gluegen-rt-2.3.2-natives-windows-i586.jar done
jars/joal-2.3.2-natives-android-aarch64.jar done
jars/joal-2.3.2-natives-android-armv6.jar done
jars/joal-2.3.2-natives-linux-amd64.jar done
jars/joal-2.3.2-natives-linux-armv6.jar done
jars/joal-2.3.2-natives-linux-armv6hf.jar done
jars/joal-2.3.2-natives-linux-i586.jar done
jars/joal-2.3.2-natives-macosx-universal.jar done
jars/joal-2.3.2-natives-solaris-amd64.jar done
jars/joal-2.3.2-natives-solaris-i586.jar done
jars/joal-2.3.2-natives-windows-amd64.jar done
jars/joal-2.3.2-natives-windows-i586.jar done
jars/jocl-2.3.2-natives-android-aarch64.jar done
jars/jocl-2.3.2-natives-android-armv6.jar done
jars/jocl-2.3.2-natives-linux-amd64.jar done
jars/jocl-2.3.2-natives-linux-armv6.jar done
jars/jocl-2.3.2-natives-linux-armv6hf.jar done
jars/jocl-2.3.2-natives-linux-i586.jar done
jars/jocl-2.3.2-natives-macosx-universal.jar done
jars/jocl-2.3.2-natives-solaris-amd64.jar done
jars/jocl-2.3.2-natives-solaris-i586.jar done
jars/jocl-2.3.2-natives-windows-amd64.jar done
jars/jocl-2.3.2-natives-windows-i586.jar done
jars/jogl-all-2.3.2-natives-android-aarch64.jar done
jars/jogl-all-2.3.2-natives-android-armv6.jar done
jars/jogl-all-2.3.2-natives-linux-amd64.jar done
jars/jogl-all-2.3.2-natives-linux-armv6.jar done
jars/jogl-all-2.3.2-natives-linux-armv6hf.jar done
jars/jogl-all-2.3.2-natives-linux-i586.jar done
jars/jogl-all-2.3.2-natives-macosx-universal.jar done
jars/jogl-all-2.3.2-natives-solaris-amd64.jar done
jars/jogl-all-2.3.2-natives-solaris-i586.jar done
jars/jogl-all-2.3.2-natives-windows-amd64.jar done
jars/jogl-all-2.3.2-natives-windows-i586.jar done
jars/linux32/gluegen-rt-2.3.2-natives-linux-i586.jar done
jars/linux32/joal-2.3.2-natives-linux-i586.jar done
jars/linux32/jocl-2.3.2-natives-linux-i586.jar done
jars/linux32/jogl-all-2.3.2-natives-linux-i586.jar done
jars/linux64/gluegen-rt-2.3.2-natives-linux-amd64.jar done
jars/linux64/joal-2.3.2-natives-linux-amd64.jar done
jars/linux64/jocl-2.3.2-natives-linux-amd64.jar done
jars/linux64/jogl-all-2.3.2-natives-linux-amd64.jar done
jars/macosx/gluegen-rt-2.3.2-natives-macosx-universal.jar done
jars/macosx/joal-2.3.2-natives-macosx-universal.jar done
jars/macosx/jocl-2.3.2-natives-macosx-universal.jar done
jars/macosx/jogl-all-2.3.2-natives-macosx-universal.jar done
jars/win32/gluegen-rt-2.3.2-natives-windows-i586.jar done
jars/win32/joal-2.3.2-natives-windows-i586.jar done
jars/win32/jocl-2.3.2-natives-windows-i586.jar done
jars/win32/jogl-all-2.3.2-natives-windows-i586.jar done
Done: Checksummer

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b18
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b18
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Program Files\Java\jdk1.8.0_66/jre
  imagej.dir => C:\Users\Public\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151222031554)
Fiji: http://update.fiji.sc/ (last check:20151222052403)
Java-8: http://sites.imagej.net/Java-8/ (last check:20151222051830)

Files not up-to-date:
  d290c110 (LOCAL_ONLY) 20151218154910 jars/commons-io-2.4.jar
  c6325009 (LOCAL_ONLY) 20151218154940 jars/omero/imagej-omero-0.3.2.jar
  1445b008 (LOCAL_ONLY) 20151218154949 jars/omero/omero-client-5.1.2-ice35.jar
  2f2a824f (LOCAL_ONLY) 20151218154950 jars/omero/scijava-log-slf4j-1.0.0.jar
  928ffe97 (LOCAL_ONLY) 20151218154912 plugins/Adapt__v1.146.jar
  8808d802 (LOCAL_ONLY) 20151218154909 plugins/BioVoxxel_Plugins.jar
  bae2315e (LOCAL_ONLY) 20151218154910 plugins/Data_Analysis.jar
  4c4c0e80 (LOCAL_ONLY) 20151218154912 plugins/IA_Class_Library_v1.123.jar
  1c348610 (LOCAL_ONLY) 20151218154911
plugins/Particle_Tracker_Library_v1.125.jar
  fe58c8cc (LOCAL_ONLY) 20151218154643 plugins/jars/nanozoomer-1.0.0.jar
  8e8db316 (LOCAL_ONLY) 20151218154907 plugins/mcib3d-suite/mcib3d-core.jar
  a4ccc1f2 (LOCAL_ONLY) 20151218154907 plugins/mcib3d-suite/mcib3d_plugins.jar

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