Package: src:picard-tools Version: 3.4.0+dfsg-1 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202606/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:picard-tools, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem=gradle --with javahelper,maven_repo_helper dh_auto_clean -O--buildsystem=gradle sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /<<BUILDDIR>>/picard-tools-3.4.0\+dfsg/.gradle /<<BUILDDIR>>/picard-tools-3.4.0\+dfsg/buildSrc/.gradle .m2 dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* Duplicate specification "u=s" for option "u" Duplicate specification "u=s" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper debian/rules override_dh_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' [... snipped ...] PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[7](GENOME_TERRITORY 200000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 200000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 400000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testForVcf(picard.vcf.processor.WidthLimitingDecoratorTest) Gradle Test Executor 1 finished executing tests. Results: FAILURE (5255 tests, 5251 successes, 4 failures, 0 skipped) 5255 tests completed, 4 failed Finished generating test XML results (0.184 secs) into: /tmp/tmp.6Wsa7YRQrL/picardTest/build/test-results/test Generating HTML test report... Finished generating test html results (0.224 secs) into: /tmp/tmp.6Wsa7YRQrL/picardTest/build/reports/tests/test :test FAILED :test (Thread[#29,Daemon worker,5,main]) completed. Took 6 mins 4.609 secs. FAILURE: Build failed with an exception. * What went wrong: Execution failed for task ':test'. > There were failing tests. See the report at: > file:///tmp/tmp.6Wsa7YRQrL/picardTest/build/reports/tests/test/index.html * Try: Run with --debug option to get more log output. Run with --scan to get full insights. * Exception is: org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':test'. at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70) at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51) at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:62) at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54) at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60) at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97) at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87) at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52) at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52) at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54) at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98) at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626) at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:59) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128) at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23) at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43) at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37) at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30) at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:314) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:204) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:134) at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:109) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78) at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75) at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152) at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100) at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75) at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28) at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35) at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40) at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47) at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39) at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57) at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36) at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43) at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:69) at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:30) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59) at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45) at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74) at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72) at org.gradle.util.Swapper.swap(Swapper.java:38) at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82) at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36) at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122) at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50) at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Caused by: org.gradle.api.GradleException: There were failing tests. See the report at: file:///tmp/tmp.6Wsa7YRQrL/picardTest/build/reports/tests/test/index.html at org.gradle.api.tasks.testing.AbstractTestTask.handleTestFailures(AbstractTestTask.java:547) at org.gradle.api.tasks.testing.AbstractTestTask.executeTests(AbstractTestTask.java:464) at org.gradle.api.tasks.testing.Test.executeTests(Test.java:530) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73) at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46) at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39) at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26) at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:780) at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:747) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92) ... 103 more * Get more help at https://help.gradle.org BUILD FAILED in 6m 15s 5 actionable tasks: 5 executed dh_auto_build: error: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=2 test returned exit code 1 make[1]: *** [debian/rules:25: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:7: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
