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Bug 663 - tracmate doesn't work after lasr update
tracmate doesn't work after lasr update
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: 2013-09-12 05:41 CDT by Fabrice Senger
Modified: 2013-09-12 13:44 CDT
3 users (show)

See Also:
Description Fabrice Senger 2013-09-12 05:41:25 CDT 
tracmate doesn't work after lasr update.
I'm running now IJ1.48b with Java 1.6.0_51 (64 bit) , on Mac os 10.6.8

Updated FIJI today...12/09/13

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_51
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_51-b11-457-10M4509
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.51-b01-457
  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 Jean-Yves Tinevez 2013-09-12 10:49:42 CDT 
Hi all

It seems that the problem is caused by a dependency problem with the imglib2-meta package. It is fixed in the master branch of imglib2. 

I would need to re-release a version of imglib2 for this. 
Is it ok to do this?
How can I do this?
Comment 2 Johannes Schindelin 2013-09-12 10:58:10 CDT 
Actually, I just forgot to upload a new TrackMate_.jar (we adjusted TrackMate to the backwards-incompatible change in ImgLib2 here: https://github.com/fiji/fiji/commit/0aa6126355ec5746e3629c235332d9c5b547deb7).

I just uploaded a new TrackMate, Jean-Yves, I hope that was okay with you?
Comment 3 Jean-Yves Tinevez 2013-09-12 11:06:27 CDT 
Actually it still does not work after updating: 

TrackMate does not pass the first step and throw the following exception:

12/09/13 18:05:09,742 [0x0-0x322322].org.fiji: Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: net.imglib2.img.ImagePlusAdapter.wrapImgPlus(Lij/ImagePlus;)Lnet/imglib2/meta/ImgPlus;
12/09/13 18:05:09,742 [0x0-0x322322].org.fiji: 	at fiji.plugin.trackmate.util.TMUtils.rawWraps(TMUtils.java:96)
12/09/13 18:05:09,742 [0x0-0x322322].org.fiji: 	at fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor.aboutToHidePanel(StartDialogDescriptor.java:109)
12/09/13 18:05:09,742 [0x0-0x322322].org.fiji: 	at fiji.plugin.trackmate.gui.TrackMateGUIController.next(TrackMateGUIController.java:806)
12/09/13 18:05:09,742 [0x0-0x322322].org.fiji: 	at fiji.plugin.trackmate.gui.TrackMateGUIController.actionPerformed(TrackMateGUIController.java:743)
12/09/13 18:05:09,742 [0x0-0x322322].org.fiji: 	at fiji.plugin.trackmate.gui.TrackMateWizard.fireAction(TrackMateWizard.java:231)
Comment 4 Jean-Yves Tinevez 2013-09-12 11:29:24 CDT 
On what version of Imglib2 should I depend?
Comment 5 Johannes Schindelin 2013-09-12 12:39:15 CDT 
sorry, I forgot that imglib2-ij is not on the ImageJ update site. I uploaded it, too.

The whole problem arose because ImgLib2 was upgraded to beta 15 on the ImageJ update site and I forgot to upgrade the corresponding files on the Fiji update site. Sorry!
Comment 6 Johannes Schindelin 2013-09-12 13:44:29 CDT 
I should have tested it before uploading, my bad. But even then, I would have forgotten about imglib2-ij being exclusively on the Fiji update site (it is a little unfortunate that ij-legacy and imglib2-ij do not share more code because parts of them do exactly the same things...).

Anyway, TrackMate works again in my hands, so I close this bug again.