beast 1.8.1 fails to parse a codonPartitionedRobustCounting element

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Oleksandr Moskalenko

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Oct 14, 2014, 6:42:32 PM10/14/14
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beast 1.8.1 (with beagle 2.1.2) on linux fails on a valid element claiming it is incorrectly constructed:

$ beast -verbose -overwrite -beagle_SSE -beagle_instances 2 -threads 4  -seed 86445293309 -errors 1000 test.xml > screen.log

beast -verbose -overwrite -beagle_SSE -beagle_instances 2 -threads 4  -seed 86445293309 -errors 1000 test.xml > screen.log 
Picked up _JAVA_OPTIONS: -Xms128m -Xmx1024m
dr.xml.XMLParseException: The '<codonPartitionedRobustCounting>' element with id, 'test.robustCounting1', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of name firstPosition REQUIRED containing
    Exactly one ELEMENT of type AncestralStateBeagleTreeLikelihood 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.parse(Unknown Source)
        at dr.app.beast.BeastMain.<init>(Unknown Source)
        at dr.app.beast.BeastMain.main(Unknown Source)



Here's the element in question. It looks fine from what I see. An xmllint run shows all required elements 
>___<!-- Robust counting for: test                                    -->
 >___<codonPartitionedRobustCounting id="test.robustCounting1" labeling="S" useUniformization="true" unconditionedPerBranch="true">
 >___>___<treeModel idref="treeModel"/>
 >___>___<firstPosition>
 >___>___>___<AncestralStateBeagleTreeLikelihood idref="CP1.treeLikelihood"/>
 >___>___</firstPosition>
 >___>___<secondPosition>
 >___>___>___<AncestralStateBeagleTreeLikelihood idref="CP2.treeLikelihood"/>
 >___>___</secondPosition>
 >___>___<thirdPosition>
 >___>___>___<AncestralStateBeagleTreeLikelihood idref="CP3.treeLikelihood"/>
 >___>___</thirdPosition>
 >___</codonPartitionedRobustCounting>
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