#575 can't load into 2beta27 platform-indep

closed-fixed
OBO-Edit (934)
5
2008-01-24
2008-01-23
No

The Mac installer version loads up GO with no problems, but the platform-independent version doesn't. I'm using the 'advanced' interface and OBO file adapter, and the initial dialog box looks normal. I click 'OK' and get a normal-looking progress bar, but at about 66% it craps out.

With 512M allocated to O-E, I just get a partly-blank version of the load dialog (shown in attached pic). If I up it to 1536M, it manages to tell me "Load error - Java heap space". This seems pretty poor, given that I can load and browse GO with 1536M in the installer version of 2b27 (and I run O-E 1.x with 768M to edit!).

Discussion

  • Midori Harris

    Midori Harris - 2008-01-23

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    p.s. and after a failed load attempt, I have to kill the java process; can't quit O-E normally

     
  • Nomi Harris

    Nomi Harris - 2008-01-23

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    Also note: although the Mac installed version includes a test_resources subdirectory, the platform-independent one lacks it, for some reason.

     
  • Karen Christie

    Karen Christie - 2008-01-23

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    Hi,

    Adding comments from my similarly failed attempts to load GO into 2beta27 platform-indep:

    I get to either 69 or 70% before it stalls. Having launched command line, I sometimes get output in my terminal window (in the last couple attempts, appearance, or not, of error messages seemed to correlate with clicking on the stalled progress window).

    Here is a sample of the error output:

    Reading [/Users/karen/Desktop/gene_ontology_edit.obo]
    java.lang.OutOfMemoryError: Java heap space
    at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:99)
    at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:575)
    at java.lang.StringBuffer.append(StringBuffer.java:321)
    at org.obo.dataadapter.OBOParseEngine.unescape(OBOParseEngine.java:1253)
    at org.obo.dataadapter.OBOParseEngine.parseTagValue(OBOParseEngine.java:565)
    at org.obo.dataadapter.OBOParseEngine.parseTag(OBOParseEngine.java:891)
    at org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:372)
    at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:43)
    at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:62)
    at org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:202)
    at org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:41)
    at org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:55)
    at org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:127)
    at org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:73)

    I also can't quit within the OBO-Edit program, but have to close the Terminal window to terminate the java process within it.

    -Karen

     
  • Nomi Harris

    Nomi Harris - 2008-01-24

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    Fixed (in b28).

     
  • Nomi Harris

    Nomi Harris - 2008-01-24

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    Fixed (in b28).

     
  • Nomi Harris

    Nomi Harris - 2008-01-24
    • status: open --> closed-fixed
     

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