Issue on saving projects

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2009-05-13
2013-05-20
  • yosuke toda
    yosuke toda
    2009-05-13

    hi,
    whenever i try to save projects, it fails.  my lab maits are all having the same problem. is it due to the language? (our environment is all in japanese) i really don't have any clue against java, so it would be helpful if you have any breakthrough. here is my environment and the saving.log with errors.

    MultiExperimentViewer - version 4.3 - Windows Vista
    Java Runtime Environment version: 1.6.0_13
    Java Runtime Environment vendor: Sun Microsystems Inc.
    Java Virtual Machine name: Java HotSpot(TM) Client VM
    Java Virtual Machine version: 11.3-b02
    Java Virtual Machine vendor: Sun Microsystems Inc.
    Java 3D Runtime Environment: Java 3D Core Runtime Environment
    Java 3D Runtime Environment vendor: Sun Microsystems, Inc.
    Java 3D Runtime Environment version:1.5.1
    Operating System name: Windows Vista
    Operating System version: 6.0
    Operating System architecture: x86

    -----------------------------
    Wed May 13 18:01:43 JST 2009
    java.lang.Exception: XMLEncoder: discarding statement ArrayList.add(FloatSlideData);
        at java.beans.XMLEncoder.writeStatement(Unknown Source)
        at java.beans.DefaultPersistenceDelegate.invokeStatement(Unknown Source)
        at java.beans.java_util_List_PersistenceDelegate.initialize(Unknown Source)
        at java.beans.PersistenceDelegate.initialize(Unknown Source)
        at java.beans.DefaultPersistenceDelegate.initialize(Unknown Source)
        at java.beans.PersistenceDelegate.writeObject(Unknown Source)
        at java.beans.Encoder.writeObject(Unknown Source)
        at java.beans.XMLEncoder.writeObject(Unknown Source)
        at org.tigr.microarray.mev.persistence.MavXMLEncoder.writeObject(MavXMLEncoder.java:30)
        at java.beans.Encoder.writeExpression(Unknown Source)
        at java.beans.XMLEncoder.writeExpression(Unknown Source)
        at java.beans.PersistenceDelegate.writeObject(Unknown Source)
        at java.beans.Encoder.writeObject(Unknown Source)
        at java.beans.XMLEncoder.writeObject(Unknown Source)
        at org.tigr.microarray.mev.persistence.MavXMLEncoder.writeObject(MavXMLEncoder.java:30)
        at java.beans.Encoder.writeObject1(Unknown Source)
        at java.beans.Encoder.cloneStatement(Unknown Source)
        at java.beans.Encoder.writeExpression(Unknown Source)
        at java.beans.XMLEncoder.writeExpression(Unknown Source)
        at java.beans.PersistenceDelegate.writeObject(Unknown Source)
        at java.beans.Encoder.writeObject(Unknown Source)
        at java.beans.XMLEncoder.writeObject(Unknown Source)
        at org.tigr.microarray.mev.persistence.MavXMLEncoder.writeObject(MavXMLEncoder.java:30)
        at java.beans.Encoder.writeObject1(Unknown Source)
        at java.beans.Encoder.cloneStatement(Unknown Source)
        at java.beans.Encoder.writeStatement(Unknown Source)
        at java.beans.XMLEncoder.writeStatement(Unknown Source)
        at java.beans.XMLEncoder.writeObject(Unknown Source)
        at org.tigr.microarray.mev.persistence.MavXMLEncoder.writeObject(MavXMLEncoder.java:30)
        at org.tigr.microarray.mev.MultipleArrayViewer$3.run(MultipleArrayViewer.java:780)
        at java.lang.Thread.run(Unknown Source)
    Caused by: java.lang.NullPointerException
        at java.beans.Encoder.cloneStatement(Unknown Source)
        at java.beans.Encoder.writeExpression(Unknown Source)
        at java.beans.XMLEncoder.writeExpression(Unknown Source)
        at java.beans.PersistenceDelegate.writeObject(Unknown Source)
        at java.beans.Encoder.writeObject(Unknown Source)
        at java.beans.XMLEncoder.writeObject(Unknown Source)
        at org.tigr.microarray.mev.persistence.MavXMLEncoder.writeObject(MavXMLEncoder.java:30)
        at java.beans.Encoder.writeObject1(Unknown Source)
        at java.beans.Encoder.cloneStatement(Unknown Source)
        at java.beans.Encoder.writeExpression(Unknown Source)
        at java.beans.XMLEncoder.writeExpression(Unknown Source)
        at java.beans.PersistenceDelegate.writeObject(Unknown Source)
        at java.beans.Encoder.writeObject(Unknown Source)
        at java.beans.XMLEncoder.writeObject(Unknown Source)
        at org.tigr.microarray.mev.persistence.MavXMLEncoder.writeObject(MavXMLEncoder.java:30)
        at java.beans.Encoder.writeObject1(Unknown Source)
        at java.beans.Encoder.cloneStatement(Unknown Source)
        at java.beans.Encoder.writeStatement(Unknown Source)
        ... 31 more

     
    • raktim
      raktim
      2009-05-13

      Hi,

      There was similar issue posted in the forum recently.
      Please take a look at it.
      https://sourceforge.net/forum/forum.php?thread_id=3121170&forum_id=378852

      In the mean time I will request our lead expert on State Saving to add any comments that she might have.

      Thanks,
      Raktim

       
      • yosuke toda
        yosuke toda
        2009-05-14

        i'll try the lastest version. hope this problem will be solved :)
        thx!
        totti

         
    • Eleanor Howe
      Eleanor Howe
      2009-05-13

      Hi there,

      Raktim's absolutely right, we've had this problem before. There are many problems with state-saving, some of which have been fixed and will be working again in our v4.4 release at the end of May. Unfortunately, I have not been able to do any work on the problem with saving datasets run on a computer with the Japanese character set. I don't have one here, so I can't test it.

      Here's what we can do, though. I've put up a snapshot of the latest development builds of MeV here: ftp://occams.dfci.harvard.edu/pub/bio/devel/mev_snapshots/ . Choose the one with the highest revision number to get the very latest (we are adding new ones every day). These versions have many state-saving improvements included in them. If the problems with saving are memory issues, this build may fix them right away. If the problems are caused by the character encoding we may at least get a better error message that may help me track down the problem. Can you try it out, and send me any errors and saving.log files that crop up? Or, if you have any information about getting Japanese characters to save properly I would appreciate that as well.

      Please keep in mind that these are development versions, however, and there may still be bugs in them. Please report any bugs you find. Thanks much!

      Eleanor

       
      • yosuke toda
        yosuke toda
        2009-05-14

        hi,
        thanks for the latest version. the problem was completely solved.
        so wonderful. :)
        thx!
        totti

         
    • yosuke toda
      yosuke toda
      2009-05-14

      hi,
      also about the japanese char issue
      char. set is also a problem against saving and loading projects, but with a little care, it can be avoided so i'll post it to inform others.

      1.japanese char should not be included in path, so running MeV under c:/ is recommended.
      2.when loading .txt files, char set should be set in Unicode(or UTF-8??). try to test few char sets when things are not going well.  SJIS char will make the project corrupt when saving...at least in my case

      :)

      totti

       
      • Sarita Nair
        Sarita Nair
        2009-05-14

        Thanks, totti. We are glad that it worked out for you. We appreciate your posting the suggestion about the japanese character issue.

         
    • Eleanor Howe
      Eleanor Howe
      2009-05-14

      Thank you, Totti, for your helpful bug reports and suggestions. I'm glad we got state-saving working for you. Thanks for helping make MeV better!

      Eleanor