Bug 975 – NoClassDefFoundError in Multi-view registration

Bug 975 - NoClassDefFoundError in Multi-view registration


Summary:	NoClassDefFoundError in Multi-view registration

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-12-11 18:00 CST by Nico Stuurman
Modified:	2014-12-16 03:47 CST
CC List:	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(AbstractImgLoader.java:131)^M
   at spim.fiji.spimdata.imgloaders.AbstractImgLoader.updateXMLMetaData(AbstractImgLoader.java:114)^M
   at spim.fiji.spimdata.imgloaders.AbstractImgLoader.updateXMLMetaData(AbstractImgLoader.java:102)^M
   at spim.fiji.plugin.Interest_Point_Detection.run(Interest_Point_Detection.java:196)^M
   at ij.IJ.runUserPlugIn(IJ.java:202)^M
   at ij.IJ.runPlugIn(IJ.java:166)^M
   at ij.Executer.runCommand(Executer.java:131)^M
   at ij.Executer.run(Executer.java:64)^M
   at java.lang.Thread.run(Thread.java:662)^M
Caused by: java.lang.ClassNotFoundException: net.imglib2.util.Pair^M
   at java.net.URLClassLoader$1.run(URLClassLoader.java:202)^M
   at java.security.AccessController.doPrivileged(Native Method)^M
   at java.net.URLClassLoader.findClass(URLClassLoader.java:190)^M
   at java.lang.ClassLoader.loadClass(ClassLoader.java:307)^M
   at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)^M
   at java.lang.ClassLoader.loadClass(ClassLoader.java:248)^M
   ... 9 more^M

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.1
  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-b14-466.1-11M4716
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-466.1
  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: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141211095341)
Fiji: http://fiji.sc/update/ (last check:20141210124822)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20141207235245)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141126030148)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20141209182639)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606082449)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526074644)
LOCI: http://sites.imagej.net/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