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Bug 879 - imagej 2 fails to load an image sequence
imagej 2 fails to load an image sequence
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-05 12:33 CDT by andrei tarasov
Modified: 2014-08-05 12:45 CDT
2 users (show)

See Also:
Description andrei tarasov 2014-08-05 12:33:18 CDT 
(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 29MB of 6093MB (<1%)
 
java.lang.NoClassDefFoundError: com/esotericsoftware/kryo/KryoSerializable
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2389)
	at java.lang.Class.getConstructor0(Class.java:2699)
	at java.lang.Class.newInstance0(Class.java:326)
	at java.lang.Class.newInstance(Class.java:308)
	at io.scif.AbstractFormat.createObject(AbstractFormat.java:207)
	at io.scif.AbstractFormat.createContextualObject(AbstractFormat.java:168)
	at io.scif.AbstractFormat.createChecker(AbstractFormat.java:116)
	at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:289)
	at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:271)
	at net.imagej.DefaultDatasetService.canOpen(DefaultDatasetService.java:224)
	at net.imagej.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:66)
	at org.scijava.io.DefaultIOService.getOpener(DefaultIOService.java:66)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:130)
	at net.imagej.legacy.DefaultLegacyHooks.interceptOpenImage(DefaultLegacyHooks.java:430)
	at ij.plugin.FolderOpener.run(FolderOpener.java:115)
	at ij.IJ.runPlugIn(IJ.java:172)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ClassNotFoundException: com.esotericsoftware.kryo.KryoSerializable
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
	... 32 more

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: UP_TO_DATE

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:20140802165300)
Fiji: http://fiji.sc/update/ (last check:20140730200634)

Files not up-to-date:
  5f458483 (OBSOLETE_UNINSTALLED) 20140224113057 jars/bio-formats-4.4.10.jar
  e1db7da8 (OBSOLETE_UNINSTALLED) 20140224113110 jars/bio-formats/scifio-4.4.10.jar
  491e89c0 (OBSOLETE_UNINSTALLED) 20130314115205 jars/forms-1.2.1.jar
  eb8dccd3 (OBSOLETE_UNINSTALLED) 20140224113046 jars/ij-app-2.0.0-beta-7.7.jar
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  f7d0e2eb (OBSOLETE_UNINSTALLED) 20140218174907 jars/ij-core-2.0.0-beta-7.7.jar
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  00efaa63 (OBSOLETE_UNINSTALLED) 20130823111139 jars/ij-launcher-2.0.2.jar
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  6e95217d (OBSOLETE_UNINSTALLED) 20140224113049 jars/ij-minimaven-2.0.0-beta-7.7.jar
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  7e2766e2 (OBSOLETE_UNINSTALLED) 20140224113048 jars/ij-platforms-2.0.0-beta-7.7.jar
  7a824b7e (OBSOLETE_UNINSTALLED) 20140224113049 jars/ij-scripting-beanshell-2.0.0-beta-7.7.jar
  433f2bc8 (OBSOLETE_UNINSTALLED) 20140224113051 jars/ij-scripting-clojure-2.0.0-beta-7.7.jar
  0a5d89fe (OBSOLETE_UNINSTALLED) 20140224113049 jars/ij-scripting-java-2.0.0-beta-7.7.jar
  de00b500 (OBSOLETE_UNINSTALLED) 20140224113052 jars/ij-scripting-javascript-2.0.0-beta-7.7.jar
  8345a4fd (OBSOLETE_UNINSTALLED) 20140224113051 jars/ij-scripting-jruby-2.0.0-beta-7.7.jar
  598d0fdf (OBSOLETE_UNINSTALLED) 20140224113051 jars/ij-scripting-jython-2.0.0-beta-7.7.jar
  351a73ce (OBSOLETE_UNINSTALLED) 20140224113050 jars/ij-text-2.0.0-beta-7.7.jar
  3cd39ba0 (OBSOLETE_UNINSTALLED) 20140224113042 jars/ij-tools-2.0.0-beta-7.7.jar
  d514e8f0 (OBSOLETE_UNINSTALLED) 20140224113043 jars/ij-ui-2.0.0-beta-7.7.jar
  b6ce787a (OBSOLETE_UNINSTALLED) 20140224113040 jars/ij-ui-common-awt-2.0.0-beta-7.7.jar
  05b1de42 (OBSOLETE_UNINSTALLED) 20140224113048 jars/ij-ui-swing-2.0.0-beta-7.7.jar
  c1ce4424 (OBSOLETE_UNINSTALLED) 20140224113049 jars/ij-ui-swing-commands-2.0.0-beta-7.7.jar
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  d4409c26 (OBSOLETE_UNINSTALLED) 20140224113040 jars/ij-ui-swing-tools-2.0.0-beta-7.7.jar
  59100d0b (OBSOLETE_UNINSTALLED) 20140218174907 jars/ij-ui-swing-updater-2.0.0-beta-7.7.jar
  4bcfadc6 (OBSOLETE_UNINSTALLED) 20140218174906 jars/ij-updater-core-2.0.0-beta-7.7.jar
  61d1660a (OBSOLETE_UNINSTALLED) 20140224113040 jars/ij-updater-ssh-2.0.0-beta-7.7.jar
  6f60a5ac (OBSOLETE_UNINSTALLED) 20140224113050 jars/ij-updater-webdav-2.0.0-beta-7.7.jar
  27161205 (OBSOLETE_UNINSTALLED) 20140224113042 jars/ij-util-awt-2.0.0-beta-7.7.jar
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  e5852db5 (OBSOLETE_UNINSTALLED) 20130823111131 jars/jai_imageio-1.0.1.jar
  da499a7d (OBSOLETE_UNINSTALLED) 20130314115206 jars/jruby.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20130314115206 jars/junit-4.8.1.jar
  cc466590 (OBSOLETE_UNINSTALLED) 20131126101646 jars/loci-common-4.4.9.jar
  e8d453ec (OBSOLETE_UNINSTALLED) 20131126101656 jars/mdbtools-java-4.4.9.jar
  70e68706 (OBSOLETE_UNINSTALLED) 20131126101653 jars/metakit-4.4.9.jar
  d12ecfe9 (OBSOLETE_UNINSTALLED) 20140303104526 jars/ome-formats-0.6.1.jar
  3aacabe8 (OBSOLETE_UNINSTALLED) 20140224113042 jars/ome-xml-4.4.10.jar
  d5a76672 (OBSOLETE_UNINSTALLED) 20131126101655 jars/poi-loci-4.4.9.jar
  eedc0cd9 (OBSOLETE_UNINSTALLED) 20130314115206 jars/serializer-2.7.1.jar
  9ae3dd1b (OBSOLETE_UNINSTALLED) 20131126101645 jars/slf4j-log4j12-1.7.2.jar
  36cdef55 (OBSOLETE_UNINSTALLED) 20130314115207 jars/xalan-2.7.1.jar
  12663f8b (LOCAL_ONLY) 20140424013044 macros/FindStackMaxima.ijm
  1447bd80 (LOCAL_ONLY) 20050408111420 plugins/3D_Deconvolution/DecCredits$1.class
  5ccdc964 (LOCAL_ONLY) 20050408111420 plugins/3D_Deconvolution/DecCredits.class
  d29fa830 (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/DeconvolutionFFT.class
  359a47eb (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/DeconvolutionSolution.class
  bb1377de (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/DeconvolutionWavelets.class
  e7854ddb (LOCAL_ONLY) 20050408111420 plugins/3D_Deconvolution/Deconvolution_.class
  63533ca6 (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/FFT1D.class
  49ea638f (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/FourierSpace.class
  d4cfb1eb (LOCAL_ONLY) 20050408140536 plugins/3D_Deconvolution/GibsonPSF.class
  330c6e0c (LOCAL_ONLY) 20050408140244 plugins/3D_Deconvolution/GibsonPSFF.class
  f4e7f902 (LOCAL_ONLY) 20050408093628 plugins/3D_Deconvolution/ImageAccess.class
  faa88a5f (LOCAL_ONLY) 20050408142652 plugins/3D_Deconvolution/OndCredits$1.class
  72630389 (LOCAL_ONLY) 20050408140014 plugins/3D_Deconvolution/OndCredits.class
  6e4486d6 (LOCAL_ONLY) 20050408140244 plugins/3D_Deconvolution/PSFCredits$1.class
  848dad8b (LOCAL_ONLY) 20050408140244 plugins/3D_Deconvolution/PSFCredits.class
  edf4dcb4 (LOCAL_ONLY) 20050408140536 plugins/3D_Deconvolution/PSFCreditsG$1.class
  3beab6cf (LOCAL_ONLY) 20050408140536 plugins/3D_Deconvolution/PSFCreditsG.class
  bf064d98 (LOCAL_ONLY) 20050408140536 plugins/3D_Deconvolution/PSF_Gibson_.class
  d6442fe6 (LOCAL_ONLY) 20050408140244 plugins/3D_Deconvolution/PSF_Simple_.class
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  0a2a5833 (LOCAL_ONLY) 20130318171846 plugins/Analyze/Colocalization_Finder.jar
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  880cc61a (LOCAL_ONLY) 20130813112017 plugins/CairnImageAnalysis.jar
  c74194a3 (LOCAL_ONLY) 20130812122448 plugins/Cairn_Image_Splitter.jar
  8d9bdfa0 (LOCAL_ONLY) 20130410164650 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  e56c4b21 (LOCAL_ONLY) 20130515230215 plugins/HandleExtraFileTypes.class
  57ec7dd6 (LOCAL_ONLY) 20130411134430 plugins/Iterative_Deconvolve_3D.class
  c19b6dc6 (LOCAL_ONLY) 20080628105856 plugins/MBF/COPYRIGHT.txt
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  3306bb2f (LOCAL_ONLY) 20040109123918 plugins/MBF/Colocalisation Analysis/ColocaliserWindow.class
  0ffc7b0c (LOCAL_ONLY) 20040203145634 plugins/MBF/Colocalisation Analysis/Colocalization_Finder.class
  a40afe7b (LOCAL_ONLY) 20050401193946 plugins/MBF/Colocalisation Analysis/Colocalization_Highligter.class
  c85511a0 (LOCAL_ONLY) 20070822131324 plugins/MBF/Colocalisation Analysis/Intensity_Correlation_Analysis.class
  c5238c99 (LOCAL_ONLY) 20090903084942 plugins/MBF/Colocalisation Analysis/Manders_Coefficients.class
  b76b8b75 (LOCAL_ONLY) 20090623094316 plugins/MBF/Colocalisation Analysis/Manders_Coefficients_4D.class
  b1954450 (LOCAL_ONLY) 20091207160738 plugins/MBF/Colocalisation Analysis/Manders_ROI_Manager.class
  6e713d0b (LOCAL_ONLY) 20070330154350 plugins/MBF/Colour functions/Align_RGB_planes.class
  a20c9cda (LOCAL_ONLY) 20070416151050 plugins/MBF/Colour functions/Colour_Balance.class
  6bbc7acd (LOCAL_ONLY) 20080104100640 plugins/MBF/Colour functions/Colour_Composite_Merge.class
  0f53fd25 (LOCAL_ONLY) 20050512174136 plugins/MBF/Colour functions/Colour_Correct.class
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  3a33950c (LOCAL_ONLY) 20050527160332 plugins/MBF/Colour functions/Resize2Rotate_.txt
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  15546ec8 (LOCAL_ONLY) 20090511154030 plugins/MBF/Colour functions/Untitled2.txt
  10854ad1 (LOCAL_ONLY) 20070126113526 plugins/MBF/Colour functions/Whiten_background.class
  7314f1c8 (LOCAL_ONLY) 20050509114822 plugins/MBF/Deconvolution/Diffraction_PSF_3D.class
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  49b8aa90 (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/ParallelSpectralDeconvolution_2D.txt
  8bbf7ed2 (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/ParallelSpectralDeconvolution_3D.txt
  0f36d33a (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/blas.jar
  6c215965 (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/f2jutil.jar
  aa4768eb (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/lapack.jar
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  0b42dba4 (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/parallelcolt-0.5.jar
  09438549 (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/parallelcolt.LICENSE.txt
  a26f0a2d (LOCAL_ONLY) 20080826172008 plugins/MBF/Deconvolution/xerbla.jar
  aa910dc7 (LOCAL_ONLY) 20040319183348 plugins/MBF/Exif_Reader.jar
  b18c6544 (LOCAL_ONLY) 20071129095620 plugins/MBF/FLIM/Batch_Convert_SDT_to_TIFF.txt
  083a784a (LOCAL_ONLY) 20090331130748 plugins/MBF/FLIM/CFP_YFP_DIC_Merge.class
  cbb58454 (LOCAL_ONLY) 20091214123242 plugins/MBF/FLIM/FLIM_Histogram$HistogramWindow.class
  18fa4c30 (LOCAL_ONLY) 20091214123242 plugins/MBF/FLIM/FLIM_Histogram.class
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  fd23f682 (LOCAL_ONLY) 20080718120426 plugins/MBF/FLIM/FLIM_stack.class
  388a3c96 (LOCAL_ONLY) 20090123140328 plugins/MBF/FLIM/LIFA_ROI_Manager.class
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  4c61a47f (LOCAL_ONLY) 20081008092914 plugins/MBF/FLIM/Open_BH_export.txt
  5600c6b2 (LOCAL_ONLY) 20091204154604 plugins/MBF/FLIM/Open_BH_export2.txt
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Comment 1 Mark Hiner 2014-08-05 12:45:00 CDT 
Please take a look a look at the "Files not up-to-date" section that was auto-generated with your bug report. You have a significant number of "OBSOLETE_UNINSTALLED" files - most notably the Bio-Formats 4.4.10 suite of jars which introduce the Kryo dependency that triggered the NoClassDefFoundError you reported.

Fiji ships with Bio-Formats 5.x right now, so at a minimum you will need to update any Bio-Formats jars. See http://fiji.sc/FAQ#Installing.2FUpdating for in-depth updating instructions. I suspect that will fix your problems.

If you still have trouble opening your data, please look through http://fiji.sc/Bug_reporting_best_practices first. Steps to reproduce the bug + a sample dataset will be very helpful to us - especially on "xxx file doesn't open" types of problems.

Thanks for the report,
Mark