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Bug 770 - can't open images (either by DND or by File>open)
can't open images (either by DND or by File>open)
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-11 02:36 CDT by Benoit Aigouy
Modified: 2014-06-11 11:51 CDT
2 users (show)

See Also:
Description Benoit Aigouy 2014-06-11 02:36:08 CDT 
here is the exception log:

File>open returns:

(Fiji Is Just) ImageJ 2.0.0-rc-4/1.49b; Java 1.6.0_24 [64-bit]; Linux 3.13.0-29-generic; 21MB of 10465MB (<1%)
 
java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;)Ljava/lang/String;
	at org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:223)
	at loci.common.NIOByteBufferProvider.<clinit>(NIOByteBufferProvider.java:88)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:129)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:138)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:147)
	at loci.common.Location.getHandle(Location.java:307)
	at loci.common.Location.getHandle(Location.java:278)
	at loci.common.Location.getHandle(Location.java:268)
	at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:95)
	at loci.formats.FormatReader.isThisType(FormatReader.java:539)
	at loci.formats.ImageReader.isThisType(ImageReader.java:245)
	at io.scif.bf.BioFormatsFormat$Checker.isFormat(BioFormatsFormat.java:201)
	at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:289)
	at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:271)
	at net.imagej.DefaultDatasetService.canOpen(DefaultDatasetService.java:215)
	at net.imagej.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:66)
	at org.scijava.io.DefaultIOService.getOpener(DefaultIOService.java:66)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:129)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:434)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:156)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.0-29-generic
  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140610234546)
Fiji: http://fiji.sc/update/ (last check:20140611000938)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526164644)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140516135525)

Files not up-to-date:
  a5d02cb7 (LOCAL_ONLY) 20131005162326 plugins/Kymo_graph1001.jar
  94ff9125 (LOCAL_ONLY) 20140126165236 plugins/Mosaic_ToolSuite/Mosaic_ToolSuite.jar
  740a32b3 (LOCAL_ONLY) 20140109112924 plugins/SplittedChannelsMerger_.class
  d31ed141 (LOCAL_ONLY) 20131016094131 plugins/Stack_Focuser_.class
  7c7e7d01 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/TA_additions/TA_plugins/Cortex.jar
  49e32d9c (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/TA_additions/TA_plugins/FlowPlugin.jar
  4646ca0d (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/TA_additions/TA_plugins/OptimizedZProjectionPlugin.jar
  dac37879 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/TA_additions/TA_plugins/QiyanPlugin.jar
  a75d5aea (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/TA_additions/TA_plugins/additionalCloneTools.jar
  efd76f39 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/TA_additions/TA_plugins/cloneRoughness.jar
  85d4afa6 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/Tissue_Analyzer.jar
  5dd9ab4f (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/changes.txt
  6341eb6e (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/compilationDate.txt
  7d5d1123 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/launcher.jar
  bdddbf0c (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/IJ.jar
  6f3fdc0d (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/Icons.jar
  21b4168a (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/IconsPA.jar
  c3cdf2d0 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/REngine.jar
  6ba3fcd5 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/Rserve.jar
  269cc20e (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/Rsession.jar
  9b7b3d20 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/batik-all-1.7.jar
  694bbee3 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/sqlite-jdbc-3.7.2.jar
  e822575d (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/lib/xml-apis-ext.jar
  3887dab6 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/license.txt
  397bab67 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/otherLicenses/licenseIcons.txt
  0f96dbd0 (LOCAL_ONLY) 20140610105127 plugins/Tissue_Analyzer/otherLicenses/licenseRsession.txt
  5f60d96e (LOCAL_ONLY) 20140306085844 plugins/Watershed_.jar
  764c419f (LOCAL_ONLY) 20140610104350 plugins/projection_/Projection_.jar
  7872d78f (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/AbsoluteLayout.jar
  e71fc299 (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/Common.jar
  bdddbf0c (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/IJ.jar
  6f3fdc0d (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/Icons.jar
  c3cdf2d0 (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/REngine.jar
  6ba3fcd5 (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/Rserve.jar
  269cc20e (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/Rsession.jar
  902be7d2 (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/ScientiFig_.jar
  9b7b3d20 (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/batik-all-1.7.jar
  e822575d (LOCAL_ONLY) 20140610104350 plugins/projection_/lib/xml-apis-ext.jar
Comment 1 Mark Hiner 2014-06-11 08:07:17 CDT 
Hi Benoit,

 Looking at the error method, I suspect there is some version skew where the wrong slf4j jar is being used.

 I can not reproduce this on my end with the update sites you have enabled. I see that you have a significant number of local .jars installed, so I assume that one of them is pulling in a conflicting slf4j dependency. The first thing I would want you to try is removing the local-only jars and seeing if you still have problems with File > Open...

If not, add your local jars back (e.g. via binary search: http://en.wikipedia.org/wiki/Binary_search_algorithm) to determine which is (or are) the offender(s).

Also, as a hunch I would try eliminating the Mosaic_ToolSuite.jar first, as it has shown to conflict with parts of core Fiji (http://fiji.sc/bugzilla/﷒0﷓, http://fiji.sc/bugzilla/﷒1﷓)
Comment 2 Benoit Aigouy 2014-06-11 11:51:19 CDT 
Hi Mark,

thanks for your comments and help. You were right, removing the mosaic tool suite folder did the job. Just as a comment, FIJI used to warn me before when I had duplicated classes (and I even think it was deleting one the duplicated jar) is it not the case any longer ?

best,

benoit