[Debian] four flaky tests in version 4.0.1

[pgrt]

Hello,

I am working on the Debian packaging of barclay. With version 4.0.1, I get 4 unit tests failing on many machines (but seemingly not all):

Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest.testEnableMultiplePlugins FAILED
org.broadinstitute.barclay.argparser.CommandLineException: requiredStringArgForPlugin is not a recognized option
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:149)
at org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest.testEnableMultiplePlugins(CommandLinePluginUnitTest.java:324)

Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest.testPluginArgumentNameCollision FAILED
org.testng.TestException:
Method CommandLinePluginUnitTest.testPluginArgumentNameCollision()[pri:0, instance:org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest@7b8d2973] should have thrown an exception of type class org.broadinstitute.barclay.argparser.CommandLineException$CommandLineParserInternalException

Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest.testPluginUsage FAILED
java.lang.AssertionError: expected [true] but found [false]
at org.testng.Assert.fail(Assert.java:94)
at org.testng.Assert.failNotEquals(Assert.java:513)
at org.testng.Assert.assertTrue(Assert.java:42)
at org.testng.Assert.assertTrue(Assert.java:52)
at org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest.testPluginUsage(CommandLinePluginUnitTest.java:246)

Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest.testRequiredDependentArguments[0](TestPluginWithRequiredArg, requiredStringArgForPlugin, fakeArgValue) FAILED
org.testng.TestException:
Method CommandLinePluginUnitTest.testRequiredDependentArguments(java.lang.String, java.lang.String, java.lang.String)[pri:0, instance:org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest@7b8d2973] should have thrown an exception of type class org.broadinstitute.barclay.argparser.CommandLineException$MissingArgument

Would you please have any idea how to solve this? Are you able to reproduce it?

Thanks a lot and best wishes,
Pierre

[cmnbroad]

@pgrt That definitely seems a bit odd - especially that its only on some machines. Those tests pass quite reliably on the Ubuntu and MacOS platforms we usually run them on, and I don't see anything obvious about them that would cause them to be flaky.

[pgrt]

Hi,

Thanks for your answer! I admit I am also puzzled by this. So far I have just patched out the tests in the Debian build as I cannot understand what is going on. We'll see...

Please feel free to close the issue if you wish, as your comment seems to indicate it is definitely not an issue with barclay...

Best wishes,
Pierre