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>