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Bug 1209 - 3D viewer doesn't launch
3D viewer doesn't launch
Product: Fiji
Classification: Unclassified
Component: Plugins
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
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(
	at java.lang.Runtime.load0(
	at java.lang.System.load(
	at com.jogamp.common.jvm.JNILibLoaderBase.loadLibraryInternal(
	at com.jogamp.common.jvm.JNILibLoaderBase.access$000(
	at com.jogamp.common.jvm.JNILibLoaderBase$DefaultAction.loadLibrary(
	at com.jogamp.common.jvm.JNILibLoaderBase.loadLibrary(
	at com.jogamp.common.os.DynamicLibraryBundle$GlueJNILibLoader.loadLibrary(
	at com.jogamp.common.os.Platform$
	at Method)
	at com.jogamp.common.os.Platform.<clinit>(
	at com.jogamp.opengl.GLProfile.<clinit>(
	at jogamp.opengl.ThreadingImpl$
	at jogamp.opengl.ThreadingImpl$
	at Method)
	at jogamp.opengl.ThreadingImpl.<clinit>(
	at com.jogamp.opengl.Threading.disableSingleThreading(
	at org.scijava.java3d.JoglPipeline.initialize(
	at org.scijava.java3d.Pipeline.createPipeline(
	at org.scijava.java3d.MasterControl.loadLibraries(
	at org.scijava.java3d.VirtualUniverse.<clinit>(
	at ij.IJ.runUserPlugIn(
	at ij.IJ.runPlugIn(
	at ij.Executer.runCommand(

Information about your version of Java:

  os.arch => x86_64 => Mac OS X
  os.version => 10.11.2
  java.version => 1.8.0_40
  java.vendor => Oracle Corporation => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_40-b25 => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.40-b25
  java.vm.vendor => Oracle Corporation => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment => 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/

Information about the version of each plugin:

Activated update sites:
ImageJ: (last check:20151222031554)
Fiji: (last check:20151222052403)
Java-8: (last check:20151222051830)
3D ImageJ Suite: (last check:20151214074914)
BioVoxxel: (last check:20151207224930)
ClearVolume: (last check:20151125184021)
ImageJ-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:

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.