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Bug 1029 - All my plugins stopped working after updating ImageJ/Fiji
All my plugins stopped working after updating ImageJ/Fiji
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-03-19 05:56 CDT by Petter Ranefall
Modified: 2015-03-20 02:20 CDT
3 users (show)

See Also:
Description Petter Ranefall 2015-03-19 05:56:17 CDT 
[ERROR] Exception
java.lang.IndexOutOfBoundsException: start 0, end 1024, s.length() 0
        at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:453) ~[na:1.6.0_24]
        at java.lang.StringBuilder.append(StringBuilder.java:179) ~[na:1.6.0_24]
        at org.scijava.plugins.scripting.java.JavaEngine.getReaderContentsAsString(JavaEngine.java:904) ~[scripting-java-0.3.0.jar:0.3.0]
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:169) ~[scripting-java-0.3.0.jar:0.3.0]
        at org.scijava.script.ScriptModule.run(ScriptModule.java:174) ~[scijava-common-2.39.0.jar:2.39.0]
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) [scijava-common-2.39.0.jar:2.39.0]
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) [scijava-common-2.39.0.jar:2.39.0]
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) [scijava-common-2.39.0.jar:2.39.0]
        at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164) [scijava-common-2.39.0.jar:2.39.0]
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) [na:1.6.0_24]
        at java.util.concurrent.FutureTask.run(FutureTask.java:138) [na:1.6.0_24]
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [na:1.6.0_24]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [na:1.6.0_24]
        at java.lang.Thread.run(Thread.java:662) [na:1.6.0_24]

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  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:\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150318211526)
Fiji: http://fiji.sc/update/ (last check:20150318211552)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150319022651)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20150219113515)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723165558)
OMERO 5.0: http://sites.imagej.net/OMERO-5.0/ (last check:20150210205446)

Files not up-to-date:
  a058df87 (LOCAL_ONLY) 20140124131224 jars/LSM_Reader.jar
  1ad3be0d (LOCAL_ONLY) 20130814112951 jars/jpedalSTD.jar
  05e8e414 (LOCAL_ONLY) 20100628140418 plugins/Colour_Deconvolution.class
  7e2df05a (LOCAL_ONLY) 20141017143922 plugins/Filters/Sobel_Convolution$FloatArray.class
  e7160f15 (LOCAL_ONLY) 20141017143922 plugins/Filters/Sobel_Convolution$FloatArray2D.class
  350f56e6 (LOCAL_ONLY) 20141017143922 plugins/Filters/Sobel_Convolution$FloatArray3D.class
  2d3455b1 (LOCAL_ONLY) 20141017143922 plugins/Filters/Sobel_Convolution.class
  e1ad1f55 (MODIFIED) 20130924134037 plugins/Gray_Morphology-2.3.2-SNAPSHOT.jar
  167adb59 (LOCAL_ONLY) 20090303131540 plugins/Histograms/CogXProfile_.class
  7aaeccc8 (LOCAL_ONLY) 20150108111533 plugins/Histograms/CompSize2DStdBrightBkg_.class
  e0d1c9ef (LOCAL_ONLY) 20150113091449 plugins/Histograms/CompSize2DStdDarkBkg_.class
  d7872e99 (LOCAL_ONLY) 20140625143057 plugins/Histograms/Components3DBothCompTree_.class
  0b1773dd (LOCAL_ONLY) 20141017132355 plugins/Histograms/Components3DInvCompTree_.class
  2f692639 (LOCAL_ONLY) 20150209112547 plugins/Histograms/FrequencyNoBkg_.class
  65e9c0c9 (LOCAL_ONLY) 20070704145400 plugins/Histograms/Frequency_.class
  a6b93598 (LOCAL_ONLY) 20141216093245 plugins/Histograms/Globals.class
  67579dde (LOCAL_ONLY) 20141217155525 plugins/Histograms/HIDE/CompSize2DInvCompTreeFast2_.class
  a280f3e9 (LOCAL_ONLY) 20141218164505 plugins/Histograms/HIDE/CompSize2DInvCompTreeFastStd_.class
  db315ccf (LOCAL_ONLY) 20141217155538 plugins/Histograms/HIDE/CompSize2DInvCompTreeFast_.class
  121c7e96 (LOCAL_ONLY) 20141218152559 plugins/Histograms/HIDE/CompSize2DInvCompTreeStd_.class
  b1e183f8 (LOCAL_ONLY) 20141216093849 plugins/Histograms/HIDE/CompSize3DInvCompTreeStd_.class
  5bc9c0b4 (LOCAL_ONLY) 20141208084503 plugins/Histograms/HIDE/CompSize3DInvCompTree_.class
  7e0f606c (LOCAL_ONLY) 20141021091158 plugins/Histograms/HIDE/SnellBrightObjects_.class
  e6fbb777 (LOCAL_ONLY) 20071030143740 plugins/Histograms/MinMaxVal_.class
  b05a271b (LOCAL_ONLY) 20141215093511 plugins/Histograms/P2Ahist_.class
  7cd68c0b (LOCAL_ONLY) 20071029095922 plugins/Histograms/YMaxLineProfile_.class
  c49ff61a (LOCAL_ONLY) 20150209091936 plugins/Histograms/YProfile3_.class
  60660b66 (LOCAL_ONLY) 20150128101045 plugins/Histograms/YProfile_.class
  2032655d (MODIFIED) 20150108103201 plugins/MTrackJ_.jar
  ef7afe1f (LOCAL_ONLY) 20130910161820 plugins/MetaImage_Reader_Writer.jar
  7f8dc054 (LOCAL_ONLY) 20071022143314 plugins/Morphology/ConnectOuter_.class
  aafd8962 (LOCAL_ONLY) 20071030103218 plugins/Morphology/ErodeTopAuto_.class
  91810432 (LOCAL_ONLY) 20071025135326 plugins/Morphology/ErodeTop_.class
  20da62a4 (LOCAL_ONLY) 20071024122342 plugins/Morphology/_2DCOGInside4Dir_.class
  9c96b915 (LOCAL_ONLY) 20070704145400 plugins/Morphology/_2DLabelSizeThr_.class
  fc1b4190 (LOCAL_ONLY) 20070704145400 plugins/Morphology/_2DLargestObject_.class
  bd272d68 (LOCAL_ONLY) 20071030163426 plugins/Morphology/_3DLabelMaxVal_.class
  b433bffb 20150213154911 plugins/Morphology/_3DLabelObjectsCompFeat_.class
  3bffe76c (LOCAL_ONLY) 20150319113103 plugins/Morphology/_3DLabelObjectsCompFeat_.jar
  94121888 (LOCAL_ONLY) 20150203082852 plugins/Morphology/_3DLabelObjects_.class
  2f5e2fa4 (LOCAL_ONLY) 20070704145400 plugins/Morphology/_3DLargestObjectPercentage_.class
  a7dfe934 (LOCAL_ONLY) 20070704145400 plugins/Morphology/_3DLargestObject_.class
  051cf47d (LOCAL_ONLY) 20070704155400 plugins/Morphology/combine_slices.class
  2f8d1fd0 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJCredits.class
  cacee973 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJEdge.class
  ee01617c (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJHierarchy.class
  e51f6692 (LOCAL_ONLY) 20140507083425 plugins/MosaicJ/MosaicJPlayField.class
  2d605607 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJStatus$1.class
  f694c43d (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJStatus$DisplayPanel.class
  a24b8ed8 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJStatus$ExportPanel.class
  bb883c12 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJStatus$ImportPanel.class
  31e70be0 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJStatus.class
  7ef6a6be (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJThumb.class
  911c8fb6 (LOCAL_ONLY) 20140507083426 plugins/MosaicJ/MosaicJTree.class
  8394440d (LOCAL_ONLY) 20140507083425 plugins/MosaicJ/MosaicJ_.class
  29f4f2c9 (LOCAL_ONLY) 20130924152416 plugins/MyExamples/TopHat2_.ijm
  19d7d0ad (LOCAL_ONLY) 20130924150616 plugins/MyExamples/TopHat2_.txt
  74045838 (LOCAL_ONLY) 20130924160022 plugins/MyExamples/TopHat3_.ijm
  7474dcca (LOCAL_ONLY) 20130924153039 plugins/MyExamples/TopHat_.ijm
  44f3f6f3 (LOCAL_ONLY) 20130902084628 plugins/NDPITools_.jar
  4fe1cfd7 (LOCAL_ONLY) 20131014124523 plugins/SNR_.jar
  c475d919 (LOCAL_ONLY) 20150316112104 plugins/Segmentation/AdaptiveSegmentationEllipseFit_.jar
  5002903f (LOCAL_ONLY) 20150316105550 plugins/Segmentation/AdaptiveSizeBasedSegmentationEllipseFitTestNonOpt_.jar
  532a4b0c (LOCAL_ONLY) 20150227132443 plugins/Segmentation/AdaptiveSizeBasedSegmentationEllipseFit_.class
  373ec52f (LOCAL_ONLY) 20150219131115 plugins/Segmentation/AdaptiveSizeBasedSegmentation_.class
  8f8f80ad (LOCAL_ONLY) 20070704145400 plugins/Segmentation/Entropy_Threshold.class
  d4156883 (LOCAL_ONLY) 20130926135141 plugins/Segmentation/FixedThreshold_.class
  07bfe8b6 (LOCAL_ONLY) 20090508081544 plugins/Segmentation/FuzzyConnectedness_.class
  28eef806 (LOCAL_ONLY) 20150225091814 plugins/Segmentation/HIDE/AdaptiveSizeBasedSegmentationEllipseFitNoBelow_.class
  1656ead0 (LOCAL_ONLY) 20150225113157 plugins/Segmentation/HIDE/AdaptiveSizeBasedSegmentationEllipseFitTest_.class
  5200bc1d (LOCAL_ONLY) 20141209135146 plugins/Segmentation/HIDE/BlobDetection_.ijm
  b94d01d5 (LOCAL_ONLY) 20150114100437 plugins/Segmentation/HIDE/BlobSegmentationDarkBkgMaxNWithinSizeIntervalPlot_.class
  bd4dbfcb (LOCAL_ONLY) 20150113110749 plugins/Segmentation/HIDE/BlobSegmentationDarkBkgMaxNWithinSizeInterval_.class
  9e0412fd (LOCAL_ONLY) 20150107105424 plugins/Segmentation/HIDE/BlobSegmentationDarkBkgPeak_.class
  eec61d97 (LOCAL_ONLY) 20150108135207 plugins/Segmentation/HIDE/BlobSegmentationDarkBkgSizeInterval_.class
  40e2e244 (LOCAL_ONLY) 20141209113412 plugins/Segmentation/HIDE/BlobSegmentation_.class
  8abb0b4c (LOCAL_ONLY) 20150219092019 plugins/Segmentation/HIDE/DynamicSizeBasedSegmentationEllipseFitDebug_.class
  37205e3d (LOCAL_ONLY) 20150210155540 plugins/Segmentation/HIDE/DynamicSizeBasedThrDebug_.class
  b25d9fd6 (LOCAL_ONLY) 20150219092012 plugins/Segmentation/HIDE/DynamicSizeBasedThr_.class
  5a90454e (LOCAL_ONLY) 20150114141944 plugins/Segmentation/HIDE/SizeBasedThrBoth_.class
  6f51d49a (LOCAL_ONLY) 20150204104153 plugins/Segmentation/HIDE/SizeBasedThrTestF_.class
  1489b9e6 (LOCAL_ONLY) 20130827095403 plugins/Segmentation/HorizontalLines_.class
  f7f6efd8 (LOCAL_ONLY) 20140204161522 plugins/Segmentation/Hough_Circles.class
  02a8fb0d (LOCAL_ONLY) 20130808090216 plugins/Segmentation/KMeans_.class
  9b494778 (LOCAL_ONLY) 20150303100526 plugins/Segmentation/Point2d.class
  b880f83a (LOCAL_ONLY) 20150305102042 plugins/Segmentation/SizeBasedThrStability_.ijm
  0846aeee (LOCAL_ONLY) 20150316114523 plugins/Segmentation/SizeBasedThr_.jar
  20561d6e (LOCAL_ONLY) 20150303100519 plugins/Segmentation/Snake.class
  ff8d3ba8 (LOCAL_ONLY) 20150303100509 plugins/Segmentation/Snake_.class
  de24ca54 (LOCAL_ONLY) 20150305143129 plugins/Segmentation/TimingThr_.ijm
  9a280aec (LOCAL_ONLY) 20130827100704 plugins/Segmentation/absnake_.jar
  8c0467d1 (LOCAL_ONLY) 20130918140925 plugins/Segmentation/adaptiveThreshold_win64.jar
  d1b9c61a (LOCAL_ONLY) 20131016141422 plugins/SignalToNoise/SNRAroundMaxima_.ijm
  3d33da65 (LOCAL_ONLY) 20131014090220 plugins/SignalToNoise/SignalToNoise_.ijm
  c17ca41c (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/Acoeffs.class
  becd5295 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/Bcoeffs.class
  f0e573b3 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/BsplineTransform.class
  f5200038 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/Convolver.class
  fa7a53dc (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/CreateMovie.class
  387b2587 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/Curve.class
  fd0f6aa0 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/DirDerrivative.class
  44343434 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/DisplayCurve.class
  9e3f40f1 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/Evaluatefunction.class
  d4b09bcc (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/Image.class
  618e23d0 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/ImageDisplay.class
  c8aeb43c (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/Iterutil.class
  a8ec6d26 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/Preferences/prefs.txt
  376bc4dd (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/Smooth.class
  56754b77 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/SplineFlowFileReader.class
  8a3c57e8 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/SplineSnakePreferences$1.class
  f7bc6f4a (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/SplineSnakePreferences$10.class
  55b3289a (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/SplineSnakePreferences$2.class
  cd29cfaf (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/SplineSnakePreferences$3.class
  b24eefcf (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/SplineSnakePreferences$4.class
  0ea6b2e0 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/SplineSnakePreferences$5.class
  aed91159 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/SplineSnakePreferences$6.class
  7426cf03 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/SplineSnakePreferences$7.class
  4cec0f05 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/SplineSnakePreferences$8.class
  d05808ab (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/SplineSnakePreferences$9.class
  af80c70c (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/SplineSnakePreferences.class
  af466097 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/dirDerDisplay.class
  da951990 (LOCAL_ONLY) 20130827101336 plugins/SplineSnake/evolveCurveDisplay.class
  bbf9d8cb (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/imageaccess/ImageAccess.class
  f06fafa2 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/imageaccess/ImageAccessStack.class
  8c30be0b (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/imageaccess/ImageAccessTools.class
  31c27e17 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/progressBarVolume.class
  e37db890 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/selectCurrentCurve.class
  5491697d (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineClearAllConstraints.class
  35789e91 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineFlowChangeFocus.class
  e3beed5d (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineFlowClearAll.class
  db954c04 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineFlowFile.class
  af7e6977 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineFlowTerminate.class
  e699fa4d (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineSnakeAction.class
  3f652947 (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineSnakeHandler.class
  8275ddd0 (LOCAL_ONLY) 20130827101338 plugins/SplineSnake/splineSnakeToolbar.class
  b7d737aa (LOCAL_ONLY) 20130827101337 plugins/SplineSnake/splineSnake_.class
  80e4afab (LOCAL_ONLY) 20141104151215 plugins/Stacks/JoinSlicesMin_.class
  2295d5ec (LOCAL_ONLY) 20140613102352 plugins/Stacks/MaxAndMinProjections_.ijm
  d46f8225 (LOCAL_ONLY) 20130808095748 plugins/Stacks/MaxMinSlicesGeneral_.class
  75c079a6 (LOCAL_ONLY) 20130816110635 plugins/Stacks/MaxMinSlicesSub2_.class
  1111ca31 (LOCAL_ONLY) 20141110103101 plugins/Stacks/MaxMinSlices_.class
  59545591 (LOCAL_ONLY) 20130807104912 plugins/Stacks/MeanSlices_.class
  b88c6574 (LOCAL_ONLY) 20140204163303 plugins/Stacks/MinSlices_.class
  3c4d7b00 (LOCAL_ONLY) 20130819134130 plugins/Stacks/SumOfNegativeSlopes_.class
  a5313d14 (LOCAL_ONLY) 20130924163926 plugins/TopHatFilterExample/TopHatFilter2_.ijm
  00e59d49 (LOCAL_ONLY) 20130924164742 plugins/TopHatFilterExample/TopHatFilter3_.ijm
  c414145c (LOCAL_ONLY) 20130924165035 plugins/TopHatFilterExample/TopHatFilter4_.ijm
  22231bed (LOCAL_ONLY) 20130924165154 plugins/TopHatFilterExample/TopHatFilter5_.ijm
  e7e08bd1 (LOCAL_ONLY) 20130924165852 plugins/TopHatFilterExample/TopHatFilter6_.ijm
  237e209e (LOCAL_ONLY) 20130924165951 plugins/TopHatFilterExample/TopHatFilter7_.ijm
  40aee2c2 (LOCAL_ONLY) 20130924165522 plugins/TopHatFilterExample/TopHatFilter8_.ijm
  5bb56891 (LOCAL_ONLY) 20150112082701 plugins/Utilities/OutlinedToFilled2_.ijm
  5393644a (LOCAL_ONLY) 20150112092548 plugins/Utilities/OutlinedToFilled_.ijm
  fb2d1ae8 (LOCAL_ONLY) 20150310135325 plugins/Vironova/EllipseSegmentation_.ijm
  5967fdf7 (LOCAL_ONLY) 20150310104414 plugins/Vironova/ExtractFoF_.ijm
  3d6e4e28 (LOCAL_ONLY) 20150310103344 plugins/Vironova/ExtractFoV_.ijm
  1b2994d4 (LOCAL_ONLY) 20150211105136 plugins/ZebraFish/MacrophagesAndNeutrophilsLeica3_.ijm
  6b71d7ab (LOCAL_ONLY) 20150303084656 plugins/ZebraFish/MacrophagesAndNeutrophilsLeica6_.ijm
  ed08d2c4 (LOCAL_ONLY) 20150213132938 plugins/ZebraFish/MacrophagesAndNeutrophilsLeica_.ijm
  2256ab4c (LOCAL_ONLY) 20150226111914 plugins/ZebraFish/MacrophagesAndNeutrophilsZeiss_.ijm
  239bbf28 (LOCAL_ONLY) 20150303084726 plugins/ZebraFish/MacrophagesAndNeutrophils_.ijm
  9c9cac5e (LOCAL_ONLY) 20140205100348 plugins/ZebraFish/StationaryLipids2_.ijm
  632194cc (LOCAL_ONLY) 20140205135510 plugins/ZebraFish/StationaryLipids3Fixed_.ijm
  feeff8b6 (LOCAL_ONLY) 20140206165657 plugins/ZebraFish/StationaryLipids3_.ijm
  1b632288 (LOCAL_ONLY) 20141111130825 plugins/ZebraFish/StationaryLipidsPreprocess_.ijm
  000c34c2 (LOCAL_ONLY) 20141110133937 plugins/ZebraFish/StationaryLipidsPreprocess_HIDE.ijm
  97495f10 (LOCAL_ONLY) 20140206132824 plugins/ZebraFish/StationaryLipidsTest_.ijm
  c733ef91 (LOCAL_ONLY) 20130919081921 plugins/ZebraFish/StationaryLipids_.ijm
  5ac6282d (LOCAL_ONLY) 20150202164457 plugins/ZebraFish/TestMAM_.ijm
  4d57b9a6 (LOCAL_ONLY) 20140206090328 plugins/ZebraFish/ZebraFishMask3_.class
  e42d07ae (LOCAL_ONLY) 20130827105819 plugins/ZebraFish/ZebraFishMask_.class
  1ad7275e (LOCAL_ONLY) 20130827133336 plugins/_2DLabelFlag_.class
  0dfa5070 (LOCAL_ONLY) 20150108103150 plugins/imagescience.jar
  16e7eed3 (LOCAL_ONLY) 20140506143046 plugins/jars/Compiler.jar
  73f557f8 (LOCAL_ONLY) 20150108103137 plugins/syndata_.jar
Comment 1 Mark Hiner 2015-03-19 08:11:21 CDT 
Hi Petter,

 Thank you for the report. Unfortunately it's not clear what plugins/scripts you were trying to execute when you got this error. Some extra information[1] about what you were trying to do would be very helpful in trying to reproduce the problem.

 Also, I see that you have a significant number of update sites and locally modified files in your Fiji installation. The locally modified files in particular could make reproducing your error impossible for others.

 You may have better luck searching through your list of plugins/update sites[2] to identify the incompatibilities.

Hope that helps.

Best,
Mark

[1] http://imagej.net/Bug_reporting_best_practices
[2] http://imagej.net/Bug_reporting_best_practices#Binary_search_through_your_external_plugins
Comment 2 Curtis Rueden 2015-03-19 12:07:39 CDT 
Petter: When you say your "plugins stopped working", you mean you can no longer successfully execute plugins from the Script Editor?

Could you please include a Minimal, Complete, Verifiable Example (http://stackoverflow.com/help/mcve) so we can reproduce? We tried, but cannot reproduce this error without more information.
Comment 3 Curtis Rueden 2015-03-19 12:11:07 CDT 
Ach, I hit "Save Changes" too soon. I actually managed to reproduce, and fix, this bug! So no more information is needed.

The bug-fix can be seen here:
https://github.com/scijava/scripting-java/commit/1e9c9fd2906c54def1adeb59c2197954db698d69

I uploaded the new version to the ImageJ update site, so update your Fiji and the bug should be gone.
Comment 4 Petter Ranefall 2015-03-20 02:20:43 CDT 
Great, now it works again. Thanks!