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danieljue / beast-mcmc

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Spurious <coalescentEventsStatistic> block inserted in log when selecting skygrid #762

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. svn up && ant (aka, compile from trunk) 
2. go through BEAUti and select the skygrid coalescent prior
3. If you try to run the generated XML you'll get something like:
"
Exactly one ELEMENT of type CoalescentIntervalProvider REQUIRED
    at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.parse(Unknown Source)
    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)
Apr 03, 2015 3:16:04 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, Dengue4.env_testskygrid.xml:
The '<coalescentEventsStatistic>' element with id, 'null', is incorrectly 
constructed.
The following was expected:
Exactly one ELEMENT of type CoalescentIntervalProvider REQUIRED
java.lang.RuntimeException: Terminate
    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)
"
The reason seems to be an empty block:
      <coalescentEventsStatistic>
      </coalescentEventsStatistic>

that is created and inserted in the log block.

Original issue reported on code.google.com by luizepid...@gmail.com on 3 Apr 2015 at 2:22