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Bug 570 - 3D Viewer will not run
3D Viewer will not run
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: 3D Viewer
unspecified
Macintosh Mac OS
: P1 critical
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-02-22 19:01 CST by Kris Sheets
Modified: 2013-04-23 12:10 CDT
2 users (show)

See Also:
Description Kris Sheets 2013-02-22 19:01:49 CST 
It was working fine in the morning Wednesday, but not in the afternoon.  When launching plugin, the error log opens but no viewer (see below for erro log contents).  Unfortunately, I can't recall all the things I was doing.  I did install the "Stack - t functions" folder of plugins from the MBF ImageJ package but later removed them.  I also believe I ran a Fiji snapshot update that day as well.

Actions tried 
1) Update of Fiji
2) Complete delete and reinstall of Fiji
3) OS X update
4) Install Java3D plugin via neurofly
5) Manuall Java3D install
6) Java update

error log

java.lang.NoClassDefFoundError: javax/media/opengl/GLCapabilitiesChooser
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
	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$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at sun.misc.Launcher$ExtClassLoader.findClass(Launcher.java:229)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:171)
	at javax.media.j3d.Pipeline$1.run(Pipeline.java:162)
	at java.security.AccessController.doPrivileged(Native Method)
	at javax.media.j3d.Pipeline.createPipeline(Pipeline.java:157)
	at javax.media.j3d.MasterControl.loadLibraries(MasterControl.java:965)
	at javax.media.j3d.VirtualUniverse.<clinit>(VirtualUniverse.java:299)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:171)
	at ij3d.Install_J3D.getJava3DVersion(Install_J3D.java:92)
	at ImageJ_3D_Viewer.checkJava3D(ImageJ_3D_Viewer.java:21)
	at ImageJ_3D_Viewer.run(ImageJ_3D_Viewer.java:13)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:148)
	at ij.Command.runCommand(Command.java:97)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ClassNotFoundException: javax.media.opengl.GLCapabilitiesChooser
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at sun.misc.Launcher$ExtClassLoader.findClass(Launcher.java:229)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 34 more

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.2
  java.version => 1.6.0_41
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_41-b02-445-11M4107
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.14-b01-445
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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Comment 1 Kris Sheets 2013-02-23 00:24:20 CST 
Backtracked version history to last working version of 3D viewer using http://jenkins.imagej.net/job/Stable-Fiji/

The last good build with a functioning 3D viewer was Build #3114 (Feb 15, 2013 9:47:43 AM).  As of Build #3115 (Feb 15, 2013 6:32:02 PM) and later, 3D viewer cannot find opengl classes in java.media.opengl 


BAD  - Build #3121 (Feb 20, 2013 4:17:40 PM)
...
BAD  - Build #3117 (Feb 18, 2013 11:49:03 AM)
...
BAD  - Build #3115 (Feb 15, 2013 6:32:02 PM)
Good - Build #3114 (Feb 15, 2013 9:47:43 AM)
Good - Build #3113 (Feb 13, 2013 4:59:27 PM)
...
Good - Build #3111 (Feb 12, 2013 4:10:28 PM)
...
Good - Build #3109 (Feb 6, 2013 2:57:46 PM)
...
Good - Build #3106 (Feb 1, 2013 5:58:18 PM)
...
Good - Build #3102 (Jan 31, 2013 12:20:57 PM)
Comment 2 Johannes Schindelin 2013-02-24 19:27:08 CST 
This is my fault, I guess, since the only updated components are the launchers.

Could you perform the following steps both in a working instance and a non-working instance: launch the Script Editor (short cut: '['), select Language>Beanshell and then execute

    print(System.getProperty("java.ext.dirs"));

and paste the output here? I will work on this as soon as I come back from vacation tomorrow.
Comment 3 Kris Sheets 2013-02-25 03:16:10 CST 
On my Mac this is the output of the Java extension directories.  Don't have access to other OS machines currently thus I cannot provide the output for different OSs.  Hopefully this is sufficient to troubleshoot. 


GOOD 3D Viewer version - Build #3114
print(System.getProperty("java.ext.dirs"));

Started New_.bsh at Sun Feb 24 18:04:14 PST 2013
/Applications/Fiji.app/java/macosx-java3d//Home/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext


BAD 3D Viewer Version - Build #3115
print(System.getProperty("java.ext.dirs"));

Started New_.bsh at Sun Feb 24 18:10:50 PST 2013
/System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/Home/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext
Comment 4 Johannes Schindelin 2013-02-25 15:25:01 CST 
Could you please overwrite Contents/MacOS/ImageJ-macosx (you will have to Ctrl-click on the Fiji application in the Finder and select 'Show Package Contents') with

http://jenkins.imagej.net/job/ImageJ-launcher/label=MacOSX/lastSuccessfulBuild/artifact/launcher/target/nar/ij-launcher-2.0.0-SNAPSHOT-x86_64-MacOSX-gcc-executable/bin/x86_64-MacOSX-gcc/ij-launcher

and test again?
Comment 5 Kris Sheets 2013-02-26 06:48:56 CST 
My apologies for the delay, I was traveling.

I downloaded the linked file.  Initially I changed the name and copied the file into MacOS/ and Fiji failed to launch.  I noticed execute permissions were not the same.  So then I added execute to user, group and other.  Fiji launched correctly then.

Results:  Using build #3115, 3D viewer launches correctly with the ij-launcher snapshot you linked to
Comment 6 Kris Sheets 2013-02-26 06:51:58 CST 
Also see bug #566.  I think this may be the same problem but it is on a Windows platform.
Comment 7 Johannes Schindelin 2013-04-23 12:10:25 CDT 
Thanks for your feedback. It seems this is resolved!