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Bug 975 - NoClassDefFoundError in Multi-view registration
NoClassDefFoundError in Multi-view registration
Product: Fiji
Classification: Unclassified
Component: Plugins
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Reported: 2014-12-11 18:00 CST by Nico Stuurman
Modified: 2014-12-16 03:47 CST
2 users (show)

See Also:

Description Nico Stuurman 2014-12-11 18:00:26 CST
Running the command Plugins> Multiview Reconstruction>Define Interest Points for Reconstruction (using any dataset) leads to the stacktrace below.  It looks to me as if the plugin has been compiled against a imglib2 version that is different from the one shipped in the current version of Fiji.  

(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49m; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 222MB of 20087MB (1%)

java.lang.NoClassDefFoundError: net/imglib2/util/Pair^M
   at spim.fiji.spimdata.imgloaders.AbstractImgLoader.updateXMLMetaData(^M
   at spim.fiji.spimdata.imgloaders.AbstractImgLoader.updateXMLMetaData(^M
   at spim.fiji.spimdata.imgloaders.AbstractImgLoader.updateXMLMetaData(^M
   at ij.IJ.runUserPlugIn(^M
   at ij.IJ.runPlugIn(^M
   at ij.Executer.runCommand(^M
Caused by: java.lang.ClassNotFoundException: net.imglib2.util.Pair^M
   at Method)^M
   at java.lang.ClassLoader.loadClass(^M
   at sun.misc.Launcher$AppClassLoader.loadClass(^M
   at java.lang.ClassLoader.loadClass(^M
   ... 9 more^M

Information about your version of Java:

  os.arch => x86_64 => Mac OS X
  os.version => 10.10.1
  java.version => 1.6.0_65
  java.vendor => Apple Inc. => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-466.1-11M4716 => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-466.1
  java.vm.vendor => Apple Inc. => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/

Information about the version of each plugin:

Activated update sites:
ImageJ: (last check:20141211095341)
Fiji: (last check:20141210124822)
3D ImageJ Suite: (last check:20141207235245)
BigDataViewer: (last check:20141126030148)
Bio-Formats: (last check:20141209182639)
FFMPEG: (last check:20130606082449)
IBMP-CNRS: (last check:20140526074644)
LOCI: (last check:20141210115338)

Files not up-to-date:
  c3f8675e (OBSOLETE_UNINSTALLED) 20140309014719 jars/Jama.jar
Comment 1 Stephan Preibisch 2014-12-16 03:47:18 CST
I uploaded a new version from the compatibility branch (which builds against imglib-2.0.0-beta26), should work now. The master branch still builds against the first stable release of imglib-2.0.0, as far as this is in Fiji, these problems should be gone.

Thanks everyone!

Cheers, Steffi