301 tests fail, 37 are skipped

[yurivict]

log

Examples of test failures from the above log:

Running Test: Test method testRequirePythonEnvironment(org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest)

Gradle suite > Gradle test > org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest > testRequirePythonEnvironment FAILED
    java.lang.NullPointerException: Cannot invoke "Object.getClass()" because the return value of "java.lang.RuntimeException.getCause()" is null
        at org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest.testRequirePythonEnvironment(StreamingPythonExecutorIntegrationTest.java:34)

Error messages in another test case:

    src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java:68: error: unmappable character (0xE2) for encoding US-ASCII
     * <li>Score : A flow-based alignment score.  Since the alignment is per-flow, in the case that there???s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.</li>
                                                                                                         ^
    src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java:68: error: unmappable character (0x80) for encoding US-ASCII
     * <li>Score : A flow-based alignment score.  Since the alignment is per-flow, in the case that there???s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.</li>
                                                                                                          ^
    src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java:68: error: unmappable character (0x99) for encoding US-ASCII
     * <li>Score : A flow-based alignment score.  Since the alignment is per-flow, in the case that there???s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.</li>
                                                                                                           ^

This test is skipped without any apparent reason:

Running Test: Test method loadIndex(org.broadinstitute.hellbender.BwaMemIntegrationTest)

Gradle suite > Gradle test > org.broadinstitute.hellbender.BwaMemIntegrationTest > loadIndex FAILED
    java.lang.UnsatisfiedLinkError: 'boolean org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createReferenceIndex(java.lang.String, java.lang.String, java.lang.String)'
        at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createReferenceIndex(Native Method)
        at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createIndexImageFromFastaFile(BwaMemIndex.java:227)
        at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createIndexImageFromFastaFile(BwaMemIndex.java:196)
        at org.broadinstitute.hellbender.BwaMemIntegrationTest.loadIndex(BwaMemIntegrationTest.java:49)
Running Test: Test method testChimericUnpairedMapping(org.broadinstitute.hellbender.BwaMemIntegrationTest)

Gradle suite > Gradle test > org.broadinstitute.hellbender.BwaMemIntegrationTest > testChimericUnpairedMapping SKIPPED
Running Test: Test method testPerfectUnpairedMapping(org.broadinstitute.hellbender.BwaMemIntegrationTest)

Gradle suite > Gradle test > org.broadinstitute.hellbender.BwaMemIntegrationTest > testPerfectUnpairedMapping SKIPPED

This test fails because some JAR wasn't built:

Running Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest)
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: No local jar was found, please build one by running


Gradle suite > Gradle test > org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest > testPipeForPicardTools STANDARD_ERROR
    No local jar was found, please build one by running
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:


Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:     /disk-samsung/ports/biology/gatk/work/gatk-4.6.0.0/gradlew localJar

        /disk-samsung/ports/biology/gatk/work/gatk-4.6.0.0/gradlew localJar
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: or

    or
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:     export GATK_LOCAL_JAR=<path_to_local_jar>

        export GATK_LOCAL_JAR=<path_to_local_jar>
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: No local jar was found, please build one by running

    No local jar was found, please build one by running
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:


Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:     /disk-samsung/ports/biology/gatk/work/gatk-4.6.0.0/gradlew localJar

etc... etc...

Version: 4.6.0.0 FreeBSD 14.1