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Bug 1264 - clearvolume broken
clearvolume broken
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-04-27 08:36 CDT by vbindoka
Modified: 2016-04-27 09:04 CDT
2 users (show)

See Also:
Description vbindoka 2016-04-27 08:36:43 CDT 
seems to be missing components:
(Fiji Is Just) ImageJ 2.0.0-rc-43/1.50i; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 1020MB of 12215MB (8%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:274)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:161)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:270)
	... 5 more
Caused by: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
	at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:81)
	at org.scijava.command.CommandModule.run(CommandModule.java:201)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	... 1 more
Caused by: java.lang.ClassNotFoundException: com.jogamp.newt.awt.NewtCanvasAWT
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 10 more

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: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: E:\MAR201~1/java/win64/jdk1.8.0_66//jre
  imagej.dir => E:\MAR201~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160422175140)
Fiji: http://update.fiji.sc/ (last check:20160418102001)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20160401010854)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20160318043608)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20160407113326)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20160210031043)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606102449)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20160418093909)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214064119)
Morphology: http://sites.imagej.net/Landini/ (last check:20160416054441)
Stowers: http://research.stowers.org/imagejplugins/updates/ (last check:20160421111233)

Files not up-to-date:
  bf461143 (LOCAL_ONLY) 20160115064746 luts/physicsBLK.lut
  6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class
  ff9106b2 (LOCAL_ONLY) 20160330133244 plugins/Adjustable_Watershed.class
  12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
  ceb27716 (LOCAL_ONLY) 20160401035706 plugins/BoneJ_.jar
  ab8a8b5e (LOCAL_ONLY) 20160108130921 plugins/CANDLE-J/CANDLE.py
  8a316fa7 (LOCAL_ONLY) 20160108130921 plugins/CANDLE-J/InverseAnscombe.class
  a72a61ac (LOCAL_ONLY) 20160108130923 plugins/CANDLE-J/NativeCodeJNA$NoiseEstimationInterface.class
  b2032c44 (LOCAL_ONLY) 20160108130923 plugins/CANDLE-J/NativeCodeJNA$ONLMInterface.class
  ff83bfd8 (LOCAL_ONLY) 20160108130923 plugins/CANDLE-J/NativeCodeJNA.class
  56b568bf (LOCAL_ONLY) 20160108130922 plugins/CANDLE-J/jna-4.1.0.jar
  7a8c0c47 (LOCAL_ONLY) 20160108130923 plugins/CANDLE-J/jna-platform-4.1.0.jar
  b0398adb (LOCAL_ONLY) 20160303104350 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
  18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
  44693e65 (LOCAL_ONLY) 20150325121214 plugins/Frac_Lac.jar
  348da731 (LOCAL_ONLY) 20141126044659 plugins/GHT_.jar
  15a0aac2 (LOCAL_ONLY) 20050408150536 plugins/GibsonPSF.class
  52861b7c (LOCAL_ONLY) 20050408150244 plugins/GibsonPSFF.class
  f481dc68 (LOCAL_ONLY) 20120817074900 plugins/Hybrid_2D_Filters.class
  6b2de3e5 (LOCAL_ONLY) 20120817084143 plugins/Hybrid_3D_Filters.class
  80c8304d (LOCAL_ONLY) 20160217091231 plugins/IHC_Toolbox.jar
  e9cb6eb7 (LOCAL_ONLY) 20150115083713 plugins/Image_CorrelationJ_1o.class
  522879f2 (LOCAL_ONLY) 20151216083238 plugins/Intensity_Correlation_Analysis.class
  d27e0bc5 (LOCAL_ONLY) 20151216105433 plugins/Intensity_Correlation_Analysis2.class
  2f3ba172 (LOCAL_ONLY) 20151222141710 plugins/Intensity_Correlation_Analysis3.class
  71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
  3589dfdf (LOCAL_ONLY) 20160317161725 plugins/MultiStackReg1.45_.jar
  21927175 (LOCAL_ONLY) 20140808090713 plugins/PIV_.jar
  b3b13b1f (LOCAL_ONLY) 20050408150244 plugins/PSFCredits$1.class
  cb99705d (LOCAL_ONLY) 20050408150244 plugins/PSFCredits.class
  de90b917 (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG$1.class
  e33950eb (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG.class
  9f2412ff (LOCAL_ONLY) 20141028082626 plugins/PSF_Generator.jar
  5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
  65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
  12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
  6208beed (LOCAL_ONLY) 20160413041704 plugins/Thunder_STORM.jar
  69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
  f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
  27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
  a0c40909 (LOCAL_ONLY) 20160414163436 plugins/colourdeconvolution.txt
  71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
  9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar
Comment 1 Curtis Rueden 2016-04-27 09:04:51 CDT 
Thanks for the report, Vytas.

ClearVolume requires the Java-8 update site to be enabled.

From the ClearVolume wiki page:

"If you use an older Fiji installation you MUST also check and install the Java-8 update site."

Alternately, you can download a fresh Fiji and it will come with Java-8 already turned on.

If you turn on the Java-8 update site and it still doesn't work, definitely let us know.