Class org.broadinstitute.hellbender.utils.python.PythonEnvironmentIntegrationTest

all > org.broadinstitute.hellbender.utils.python > PythonEnvironmentIntegrationTest

tests

failures

ignored

11.490s

duration

85%

successful

Failed tests
Tests
Standard error

Failed tests

testGATKPythonEnvironmentPackagePresent[0](mkl, 2.4.0)

java.lang.AssertionError: The installed version of mkl does not match the 2.4.0 version that was requested. Check the build log to see the actual version that was resolved by conda.
	at org.testng.Assert.fail(Assert.java:110)
	at org.broadinstitute.hellbender.utils.python.PythonEnvironmentIntegrationTest.testGATKPythonEnvironmentPackagePresent(PythonEnvironmentIntegrationTest.java:80)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

testGATKPythonEnvironmentPackagePresent[3](torch, 2.1.0.post100)

java.lang.AssertionError: The installed version of torch does not match the 2.1.0.post100 version that was requested. Check the build log to see the actual version that was resolved by conda.
	at org.testng.Assert.fail(Assert.java:110)
	at org.broadinstitute.hellbender.utils.python.PythonEnvironmentIntegrationTest.testGATKPythonEnvironmentPackagePresent(PythonEnvironmentIntegrationTest.java:80)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

Tests

Test	Duration	Result
testGATKPythonEnvironmentPackageMKLEnabled[0](pytensor, '-lmkl_rt' in pytensor.config.blas__ldflags)	1.366s	passed
testGATKPythonEnvironmentPackageMKLEnabled[1](torch, 'BLAS_INFO=mkl' in torch.__config__.show() and 'USE_MKL=ON' in torch.__config__.show())	1.132s	passed
testGATKPythonEnvironmentPackagePresent[0](mkl, 2.4.0)	0.049s	failed
testGATKPythonEnvironmentPackagePresent[10](argparse, null)	0.045s	passed
testGATKPythonEnvironmentPackagePresent[11](gcnvkernel, null)	3.099s	passed
testGATKPythonEnvironmentPackagePresent[1](numpy, 1.26.2)	0.125s	passed
testGATKPythonEnvironmentPackagePresent[2](pytensor, 2.18.1)	1.320s	passed
testGATKPythonEnvironmentPackagePresent[3](torch, 2.1.0.post100)	1.135s	failed
testGATKPythonEnvironmentPackagePresent[4](scipy, 1.11.4)	0.125s	passed
testGATKPythonEnvironmentPackagePresent[5](pymc, 5.10.0)	2.033s	passed
testGATKPythonEnvironmentPackagePresent[6](h5py, 3.10.0)	0.134s	passed
testGATKPythonEnvironmentPackagePresent[7](sklearn, 1.3.2)	0.391s	passed
testGATKPythonEnvironmentPackagePresent[8](matplotlib, 3.8.2)	0.180s	passed
testGATKPythonEnvironmentPackagePresent[9](pandas, 2.1.3)	0.356s	passed

Standard error

18:10:24.612 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-982536064.txt
18:10:25.979 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1552838564.txt
18:10:27.112 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--955343844.txt
18:10:27.168 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-467545944.txt
18:10:27.289 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1932931279.txt
18:10:28.610 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--756844624.txt
18:10:29.749 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1378549036.txt
18:10:29.871 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-568121630.txt
18:10:31.904 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1537751851.txt
18:10:32.038 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--2963386.txt
18:10:32.430 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-506871006.txt
18:10:32.610 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1989562845.txt
18:10:32.966 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-701161358.txt
18:10:33.011 INFO  StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-904763077.txt