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Bug 1151 - XMml files not readable, throw an error
XMml files not readable, throw an error
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-08-28 08:50 CDT by Akanksha
Modified: 2015-09-29 14:00 CDT
2 users (show)

See Also:
Description Akanksha 2015-08-28 08:50:24 CDT 
The updated fiji throws an exception while trying to open Xml files with BigData Viewer or the Multiview reconstruction Plugins. Here is the exception generated while trying to open with the Bigdata Viewer.

(Fiji Is Just) ImageJ 2.0.0-rc-36/1.50a; Java 1.6.0_24 [64-bit]; Linux 2.6.32-504.23.4.el6.x86_64; 45MB of 95891MB (<1%)
 
java.lang.NoClassDefFoundError: Could not initialize class org.jdom2.input.sax.XMLReaders
	at org.jdom2.input.SAXBuilder.<init>(SAXBuilder.java:338)
	at org.jdom2.input.SAXBuilder.<init>(SAXBuilder.java:221)
	at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:39)
	at bdv.BigDataViewer.open(BigDataViewer.java:459)
	at bdv.BigDataViewer.view(BigDataViewer.java:670)
	at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:108)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:132)
	at ij.Executer.run(Executer.java:65)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.32-504.23.4.el6.x86_64
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/ajain/Desktop/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/ajain/Desktop/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150827150954)
Fiji: http://update.fiji.sc/ (last check:20150826162017)
Comment 1 Curtis Rueden 2015-08-28 11:38:23 CDT 
Thanks for the bug report, Akanksha!

Please update Fiji and try again. The updater should want to remove jars/jdom.jar and jars/jdom-contrib.jar. After that, I am hoping this problem disappears. Either way, please report back.
Comment 2 Curtis Rueden 2015-09-29 14:00:42 CDT 
Presuming fixed. Please reopen if not.