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Bug 1209 - 3D viewer doesn't launch
3D viewer doesn't launch
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-12-23 08:19 CST by Felix
Modified: 2016-01-05 13:43 CST
3 users (show)

See Also:

Description Felix 2015-12-23 08:19:48 CST
I just updated according to the latest post "The roead to Java8".

Then I opened the Fly Brain sample
.. and launched the 3D viewer

that throws the following error:

java.lang.UnsatisfiedLinkError: Can't load library: //natives/macosx-universal//gluegen-rt
	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1825)
	at java.lang.Runtime.load0(Runtime.java:809)
	at java.lang.System.load(System.java:1086)
	at com.jogamp.common.jvm.JNILibLoaderBase.loadLibraryInternal(JNILibLoaderBase.java:624)
	at com.jogamp.common.jvm.JNILibLoaderBase.access$000(JNILibLoaderBase.java:63)
	at com.jogamp.common.jvm.JNILibLoaderBase$DefaultAction.loadLibrary(JNILibLoaderBase.java:106)
	at com.jogamp.common.jvm.JNILibLoaderBase.loadLibrary(JNILibLoaderBase.java:487)
	at com.jogamp.common.os.DynamicLibraryBundle$GlueJNILibLoader.loadLibrary(DynamicLibraryBundle.java:421)
	at com.jogamp.common.os.Platform$1.run(Platform.java:317)
	at java.security.AccessController.doPrivileged(Native Method)
	at com.jogamp.common.os.Platform.<clinit>(Platform.java:287)
	at com.jogamp.opengl.GLProfile.<clinit>(GLProfile.java:146)
	at jogamp.opengl.ThreadingImpl$1.run(ThreadingImpl.java:83)
	at jogamp.opengl.ThreadingImpl$1.run(ThreadingImpl.java:66)
	at java.security.AccessController.doPrivileged(Native Method)
	at jogamp.opengl.ThreadingImpl.<clinit>(ThreadingImpl.java:66)
	at com.jogamp.opengl.Threading.disableSingleThreading(Threading.java:164)
	at org.scijava.java3d.JoglPipeline.initialize(JoglPipeline.java:130)
	at org.scijava.java3d.Pipeline.createPipeline(Pipeline.java:92)
	at org.scijava.java3d.MasterControl.loadLibraries(MasterControl.java:837)
	at org.scijava.java3d.VirtualUniverse.<clinit>(VirtualUniverse.java:274)
	at ij3d.ImageJ3DViewer.run(ImageJ3DViewer.java:39)
	at ij3d.ImageJ_3D_Viewer.run(ImageJ_3D_Viewer.java:16)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:136)
	at ij.Executer.run(Executer.java:65)
	at java.lang.Thread.run(Thread.java:745)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.11.2
  java.version => 1.8.0_40
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_40-b25
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.40-b25
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  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: /Library/Java/JavaVirtualMachines/jdk1.8.0_40.jdk/Contents/Home/jre
  imagej.dir => /Users/turf/Sources/Vaa3D/vaa3d_tools/released_plugins/v3d_plugins/open_fiji/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)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20151214074914)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20151207224930)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20151125184021)
ImageJ-MATLAB: http://sites.imagej.net/MATLAB/ (last check:20151012182000)

Files not up-to-date:
  f28a1c8a (LOCAL_ONLY) 20151027115623 plugins/3d-oc_.jar
  23ed2d15 (LOCAL_ONLY) 20151028222346 plugins/analysis_3d.jar
  6355e032 (LOCAL_ONLY) 20151021191302 plugins/jars/nanozoomer-1.0.0.jar
  e0f10e71 (LOCAL_ONLY) 20150928165138 plugins/jars/ndpi-tools-5.12.3.jar
  f9e0149c (LOCAL_ONLY) 20151102155332 plugins/jars/ratiometrics-1-1.0.1-SNAPSHOT.jar
  e4479d47 (LOCAL_ONLY) 20150806131626 plugins/raw_writerBRL.class
  a9a44b30 (LOCAL_ONLY) 20150806131628 plugins/v3draw_io_imagejBRL/readme_how_to_build.txt
Comment 1 Mark Hiner 2015-12-23 09:07:49 CST
Thanks Felix.

This crash is due to the ClearVolume update site which seems to ship its own copy of 3D native libraries that are conflicting with the new Java-8 update site.

I created a section on the news post where we can document conflicts like this:
http://imagej.net/2015-12-22_-_The_road_to_Java_8#Conflicting_Update_Sites

For the short term it looks like you'll have to choose between Java-8 and ClearVolume.

Thanks for the report.
Comment 2 Felix 2015-12-28 03:34:41 CST
Yep, after removing the Clear Volume update site, the problem did not re-occur. I had to remove the update-site and restart Fiji twice though before the changes became persistent.

thanks for your help Mark
Comment 3 Curtis Rueden 2016-01-05 13:43:47 CST
I am closing this, since it is not a problem with the core ImageJ update sites, per se.

Regarding when it will be fixed on the ClearVolume side: the maintainers are already aware of this clash, and I'm sure it will be resolved within the next few months, especially as ImageJ and Fiji switch to Java 8 with the Java-8 update site on by default.