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Bug 703 - Trackmate Update 19 Feb 2014 - missing class definition
Trackmate Update 19 Feb 2014 - missing class definition
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-02-19 17:50 CST by Kris Sheets
Modified: 2014-08-24 13:24 CDT
3 users (show)

See Also:
Description Kris Sheets 2014-02-19 17:50:11 CST 
(Fiji Is Just) ImageJ 1.48r; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.1; 97MB of 11887MB (<1%)
 
java.lang.NoClassDefFoundError: net/imglib2/meta/ImgPlusMetadata
	at fiji.plugin.trackmate.TrackMatePlugIn_.createTrackMate(TrackMatePlugIn_.java:114)
	at fiji.plugin.trackmate.TrackMatePlugIn_.run(TrackMatePlugIn_.java:61)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.ClassNotFoundException: net.imglib2.meta.ImgPlusMetadata
	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:306)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 7 more

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.1
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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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  8974a54e 20140219153644 plugins/spim_viewer-1.0.0-SNAPSHOT.jar
  14eaf670 20131107133634 plugins/visad-lite-2.0.20070828.jar
  574cdfce 20131107133635 plugins/visbio_plugins-1.0-SNAPSHOT.jar
  34b7341d 20130215095012 retro/backport-util-concurrent-3.1.jar
  8759ba20 20130507174632 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 20130507174642 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 20130215095012 scripts/InstallJava3D.m
  05a92a3c 20130215095012 scripts/IsJava3DInstalled.m
  ff34d026 20130215095012 scripts/Matlab3DViewerDemo_1.m
  25be149f 20130215095012 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20130215095012 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20130215095012 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20130215095012 scripts/Miji.m
  868cd434 20130215095012 scripts/Miji_Test.m
  dc94c3a3 20130215095012 scripts/bfopen.m
  a77cab39 20130808231159 scripts/importTrackMateTracks.m
  41af04e2 20131107133852 scripts/very_basic_camera_test.bsh
Comment 1 Johannes Schindelin 2014-03-05 15:45:31 CST 
When calling Plugins>Utilities>Find Jar For Class with net.imglib2.meta.ImgPlusMetadata, I get the message:

The class net.imglib2.meta.ImgPlusMetadata is contained in /Applications/Fiji.app/jars/imglib2-meta-2.0.0-beta-25.jar

Since that file was uploaded recently, it might imply that uploading a new ImgLib2 version fixed your problem. What is your current status? Does it still occur?
Comment 2 Johannes Schindelin 2014-03-06 04:10:14 CST 
J-Y, maybe we should stop shadowing ImgLib2 on the TrackMate-dev update site? Or update to beta-25?
Comment 3 Jean-Yves Tinevez 2014-03-06 04:12:15 CST 
Let's upgrade. 
When the RC period is over, imglib2-meta-beta25 will go to the imagej repo, and TrackMate-2.2.0 to the fiji repo, right?
Comment 4 Johannes Schindelin 2014-03-06 04:35:39 CST 
Correct. For the moment, however, imglib2-meta beta-25 is uploaded to the Fiji update site -- unless my updater lies to me... ;-)
Comment 5 Jean-Yves Tinevez 2014-03-06 04:40:59 CST 
Whoooops. Could you make it right? If I do ... things will not be right.
Comment 6 Kris Sheets 2014-03-06 12:29:26 CST 
Sorry for the tardy response

I had the TrackMate-dev site enabled in the Fiji updater.  I have the 2.2.0-rc3 version installed and it is listed as the latest update from that site, as listed in the details of the updater. The problem seems to be a call to net.imglib2.meta.ImgPlusMetadata from fiji.plugin.trackmate.TrackMatePlugIn_.createTrackMate(TrackMatePlugIn_.java:114)

As the problems occurred on my 19 Feb 2014 update, inspection of the updater details for imglib2 shows the two following jars were modified.

jars/imglib2-algorithms-gpl-2.0.0-beta-23.jar
Release date:
19 Feb 2014
jars/imglib2-algorithms-legacy-2.0.0-beta-23.jar
Release date:
19 Feb 2014

I completely deleted Fiji and reinstalled fresh.  Trackmate is now running. Maybe there was some conflict of other plugins that I had installed or update sites I had enabled.