running examples :: Error

[EricDeveaud]

Hello

after build beast from the last beast-mcmc git repo (commit 2589e1ae047aa1e25da78cd26024d3fca2c834ed) build was performed using ant/1.10.7 graalvm/ce-java8-20.0.0

I tried to run randoms functional tests using or not beagle-lib/3.1.2 from the examples dir and got error on some of them with SEVERE: Parsing error - poorly formed BEAST file

see for example

[gensoft@55c39a5bf82f examples]$ pwd
/opt/gensoft/src/beast-mcmc/beast-mcmc-1.10.5-23570d1/examples
[gensoft@55c39a5bf82f examples]$ java -jar ../build/dist/beast.jar -overwrite Recombination/arg-rokas.xml  |& tail -10
  with initial relative rate = 1.0
  4 category discrete gamma with initial shape = 0.5
Dec 04, 2020 3:20:13 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, arg-rokas.xml:
The '<argTreeLikelihood>' element, with id, 'treeLikelihood1', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type SiteModel REQUIRED

Error thrown at: dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

[gensoft@55c39a5bf82f examples]$ java -jar  -Djava.library.path=/opt/gensoft/lib/beagle-lib/3.1.2/lib ../build/dist/beast.jar -overwrite Calibrations/constrainedTaxaTest1.xml 2>&1  | tail -n 10
Creating the tree model, 'treeModel'
  taxon count = 3
  tree height = 98.41989967066743
Dec 04, 2020 3:18:57 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, constrainedTaxaTest1.xml:
Error parsing '<scaleOperator>' element with id, 'null':
Scale operator can only be used on parameters with an infinite upper or lower bound (use a RandomWalk) (xx)

Error thrown at: dr.inferencexml.operators.ScaleOperatorParser.parseXMLObject(Unknown Source)

is my build broken, or are the examples files incorrect ?

regards

Eric

[rambaut]

Many of the examples may be out of date and need refreshing. Will add a separate issue.