Some tests are failing in ANT, but not in IDE

[J-Moravec]

TreeLikelihoodWithErrorFastTest and TreeLikelihoodWithErrorSlowTest are failing, but only with the ANT build, not in IDE.

Possible it is my computer only, because of some weird interaction and does not happen in a clean environment.

[J-Moravec]

Same with Gradle. Possible reason:

It seems that the when building in command line, Beagle library is used:

phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorSlowTest > testGT16ErrorLikelihoodCase1 FAILED
    junit.framework.AssertionFailedError: expected:<-5.107125869350904> but was:<-6.0096031993688195>
        at junit.framework.Assert.fail(Assert.java:57)
        at junit.framework.Assert.failNotEquals(Assert.java:329)
        at junit.framework.Assert.assertEquals(Assert.java:120)
        at junit.framework.Assert.assertEquals(Assert.java:129)
        at phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorSlowTest.testGT16ErrorLikelihoodCase1(TreeLikelihoodWithErrorSlowTest.java:529)

phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorSlowTest > testBinaryLikelihoodSmallNoError STANDARD_OUT
    a: 1 2
    b: 1 2
    Alignment(null)
      2 taxa
      1 site

      Using BEAGLE version: 3.2.0 (PRE-RELEASE) resource 0: CPU
        with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

While when build in IDE, Beagle is not used:

phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorSlowTest > testGT16ErrorLikelihoodCase1 STANDARD_OUT
    a: 1 16
    b: 1 16
    Alignment(null)
      2 taxa
      1 site

phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorSlowTest > testGT16ErrorLikelihoodCase1 STANDARD_ERROR
    Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path: /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib

[kche309]

@J-Moravec thanks for looking into this. I will be adding a fix to use the non-Beagle version by default.

The current version tries to use Beagle if it detects a Beagle on your system, but error model classes are not Beagle compatible. Starting Beast with the -java option will ensure the correct version is used, I've added a note in the readme for this step.

[J-Moravec]

@kche309 I think the issue is in the parent class's method initAndValidate: https://github.com/CompEvol/beast2/blob/518a0ed4178425251690365bd1379afd46719c17/src/beast/evolution/likelihood/TreeLikelihood.java#L144-L159

Beagle is initialized, even if the TreeLikelihoodWithError doesn't support it. Overriding this step could help it. Not sure how -java switch is managing to do that internally. Otherwise, exposing it (i.e., implementing some kind of switch, such as useBeagle=true set by default, with the child class) to the TreeLikelihood might be a better solution.

        beagle = null;
        beagle = new BeagleTreeLikelihood();
        try {
            beagle.initByName(
                    "data", dataInput.get(), "tree", treeInput.get(), "siteModel", siteModelInput.get(),
                    "branchRateModel", branchRateModelInput.get(), "useAmbiguities", m_useAmbiguities.get(), 
                    "useTipLikelihoods", m_useTipLikelihoods.get(),"scaling", scaling.get().toString());
            if (beagle.beagle != null) {
                //a Beagle instance was found, so we use it
                return;
            }
        } catch (Exception e) {
            // ignore
        }
        // No Beagle instance was found, so we use the good old java likelihood core
        beagle = null;

[kche309]

@J-Moravec Yes, that's right. There's a system beagle flag I can set to achieve the same behaviour as the java flag. I will add this to both the TreeLikelihood error classes.

[kche309]

The Beagle error message should be fixed for gradle2 by https://github.com/bioDS/beast-phylonco/commit/9416241fca73acd0b220167ee734bf64aad2328c