Class org.broadinstitute.hellbender.utils.python.PythonEnvironmentIntegrationTest
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)
testGATKPythonEnvironmentPackagePresent[4](scipy, 1.11.4)
java.lang.AssertionError: The installed version of scipy does not match the 1.11.4 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) |
1.275s |
passed |
| testGATKPythonEnvironmentPackageMKLEnabled[1](torch, 'BLAS_INFO=mkl' in torch.__config__.show() and 'USE_MKL=ON' in torch.__config__.show()) |
1.114s |
passed |
| testGATKPythonEnvironmentPackagePresent[0](mkl, 2.4.0) |
0.048s |
failed |
| testGATKPythonEnvironmentPackagePresent[10](argparse, null) |
0.046s |
passed |
| testGATKPythonEnvironmentPackagePresent[11](gcnvkernel, null) |
2.997s |
passed |
| testGATKPythonEnvironmentPackagePresent[1](numpy, 1.26.2) |
0.118s |
passed |
| testGATKPythonEnvironmentPackagePresent[2](pytensor, 2.18.1) |
1.260s |
passed |
| testGATKPythonEnvironmentPackagePresent[3](torch, 2.1.0.post100) |
1.104s |
failed |
| testGATKPythonEnvironmentPackagePresent[4](scipy, 1.11.4) |
0.114s |
failed |
| testGATKPythonEnvironmentPackagePresent[5](pymc, 5.10.0) |
1.942s |
passed |
| testGATKPythonEnvironmentPackagePresent[6](h5py, 3.10.0) |
0.124s |
passed |
| testGATKPythonEnvironmentPackagePresent[7](sklearn, 1.3.2) |
0.429s |
passed |
| testGATKPythonEnvironmentPackagePresent[8](matplotlib, 3.8.2) |
0.171s |
passed |
| testGATKPythonEnvironmentPackagePresent[9](pandas, 2.1.3) |
0.350s |
passed |
Standard error
15:45:18.369 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--358002938.txt
15:45:19.645 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--107178967.txt
15:45:20.760 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--432358748.txt
15:45:20.814 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1829691885.txt
15:45:20.930 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1664433094.txt
15:45:22.190 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-371745558.txt
15:45:23.295 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1285643490.txt
15:45:23.412 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-717370979.txt
15:45:25.351 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1703740114.txt
15:45:25.476 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-1334148810.txt
15:45:25.905 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal-502384548.txt
15:45:26.076 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--599897519.txt
15:45:26.426 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--754456586.txt
15:45:26.472 INFO StreamingProcessController - Enabling streaming process journaling file gatkStreamingProcessJournal--1194705393.txt