Bug#1139484: marked as done (picard-tools: FTBFS: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference)
"Debian Bug Tracking System" <[email protected]> Tue, 04 Aug 2026 09:07:07 +0000
| Newsgroups | gmane.linux.debian.devel.bugs.rc |
|---|---|
| Message-ID | <handler.1139484.D1139484.17858342623317937.ackdone@bugs.debian.org> |
This is a multi-part message in MIME format... ------------=_1785834427-3318911-0 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your message dated Tue, 04 Aug 2026 09:04:19 +0000 with message-id <[email protected]> and subject line Bug#1139484: fixed in picard-tools 3.5.0+dfsg-1 has caused the Debian Bug report #1139484, regarding picard-tools: FTBFS: Test: Test method testCleanSam[1](simple_ove= rhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignor= ing SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_= overhang, Read CIGAR M operator maps off end of reference to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) --=20 1139484: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=3D1139484 Debian Bug Tracking System Contact [email protected] with problems ------------=_1785834427-3318911-0 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by bugs.debian.org; 9 Jun 2026 09:47:56 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-120.0 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FROMDEVELOPER,HAS_PACKAGE,MONEY, SPF_HELO_PASS,SPF_PASS,STOCKLIKE,USER_IN_DKIM_WELCOMELIST,X_DEBBUGS_CC autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 51; hammy, 150; neutral, 987; spammy, 0. spammytokens: hammytokens:0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--HTo:N*Debian, 0.000-+--forky, 0.000-+--H*F:U*sanvila Return-path: <[email protected]> Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72]:44192) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <[email protected]>) id 1wWt3s-00BduC-0G for [email protected]; Tue, 09 Jun 2026 09:47:56 +0000 Received: via submission from C=NA,ST=NA,L=Ankh Morpork,O=Debian SMTP,OU=Debian SMTP CA,CN=paradis.debian.org,[email protected] (verified) by mailly.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <[email protected]>) id 1wWt3q-00BN62-1y for [email protected]; Tue, 09 Jun 2026 09:47:54 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.paradis; h=Date:Message-Id:Subject:To:From:Reply-To:Cc: MIME-Version:Content-Type:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=sKplK2kaI2zyCE2EbwG16g+Umi0dV0KMAowGy4lLbFI=; b=HeFXCbaH81vb6ntuar7/hJCPCM 92fljuV1lfjzD2OugsPpFj8EwdaG3AuPhhvrjFEg84QjrYBMll0vJ9UwFrbGvS/gqgDstTRhQnOhs scrvWierVnesWQZGrPMREKQGoKyMw3o3Ymq8QCIQPe7n6d4OShKMb8N17HNj79/uCj6bf3W9MPdwP xA+A82BirlJnbi0TRL4prxM/DB9PdNG/Nr17nIJKb9wj+gUtsR3adVOf7F3bowfBAa3y2lY6Y4NBB F6GICRYRrqqRveymEPYeqD9dHd4pra0uMqLip2TJgc/+5UYXvr8JujlB8Qfq6pxy8XrJsD5RGERCK EklXqqBg==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <[email protected]>) id 1wWt3p-00ApDE-16 for [email protected]; Tue, 09 Jun 2026 09:47:53 +0000 From: Santiago Vila <[email protected]> To: Debian BTS <[email protected]> Subject: picard-tools: FTBFS: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference X-Debbugs-Cc: [email protected] Message-Id: <[email protected]> Date: Tue, 09 Jun 2026 09:47:53 +0000 Delivered-To: [email protected] 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 -------------------------------------------------------------------------------- ------------=_1785834427-3318911-0 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 1139484-close) by bugs.debian.org; 4 Aug 2026 09:04:22 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-110.7 required=4.0 tests=ALL_TRUSTED,BAYES_00, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FVGT_m_MULTI_ODD, HAS_BUG_NUMBER,MD5_SHA1_SUM,MEDS2,PDS_BTC_ID,PGPSIGNATURE, SPF_HELO_PASS,SPF_PASS,USER_IN_DKIM_WELCOMELIST,WORD_WITHOUT_VOWELS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 96; hammy, 150; neutral, 165; spammy, 0. spammytokens: hammytokens:0.000-+--HX-Debian:DAK, 0.000-+--H*rp:D*ftp-master.debian.org, 0.000-+--HX-DAK:process-upload, 0.000-+--UD:debian.tar.xz, 0.000-+--H*r:sk:fasolo. Return-path: <[email protected]> Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72]:53310) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <[email protected]>) id 1wrB4Q-00Dv8x-06 for [email protected]; Tue, 04 Aug 2026 09:04:22 +0000 Received: via submission from C=NA,ST=NA,L=Ankh Morpork,O=Debian SMTP,OU=Debian SMTP CA,CN=fasolo.debian.org,[email protected] (verified) by mailly.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <[email protected]>) id 1wrB4O-000JdM-1m for [email protected]; Tue, 04 Aug 2026 09:04:20 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=ftp-master.debian.org; s=smtpauto.fasolo; h=Date:Message-Id:Content-Type: Subject:MIME-Version:To:Reply-To:From:Cc:Content-Transfer-Encoding:Content-ID :Content-Description:In-Reply-To:References; bh=VuaRn7dqU1i/yYPVeqYkwxIwRHpCvJGg8Do3s2XEe40=; b=cRpYAvwNXHXSaBzx+h6FowO1dl CyQwZvO5HCv5SR8R/l2HeCcAX1Xbt5UNQfczBlx0Bd679FMbi5+2QAaYw9YE335+4zRklNDjK9lym 0KcSnjNJJKx4TimX67qaYbvdaGqtc0CCc2ucOwuKcS5kqhIAvefpQ4POwdQJcxzmKD3Wljtf3jzxs Lh1FSCXGrtFz97M5yGiXQg6GF2KLX03igSQRRFIFE1NSoXhy5yZsrmQQoyuFBj1XQqT0OBbts0/1p zz4Wf1aqHV73ijAWVdDZpHHCi2w0M2MsW4gTy6FgtVwOXvzHYC5aV1IPV5neItav9oKB/hoxAFZXN dk02VXew==; Received: from dak by fasolo.debian.org with local (Exim 4.98.2) (envelope-from <[email protected]>) id 1wrB4N-0000000A7fG-2dRo; Tue, 04 Aug 2026 09:04:19 +0000 From: Debian FTP Masters <[email protected]> Reply-To: Pierre Gruet <[email protected]> To: [email protected] X-DAK: dak process-upload X-Debian: DAK X-Debian-Package: picard-tools Debian: DAK Debian-Changes: picard-tools_3.5.0+dfsg-1_source.changes Debian-Source: picard-tools Debian-Version: 3.5.0+dfsg-1 Debian-Architecture: source Debian-Suite: unstable Debian-Archive-Action: accept MIME-Version: 1.0 Subject: Bug#1139484: fixed in picard-tools 3.5.0+dfsg-1 Content-Type: multipart/signed; micalg="pgp-sha256"; protocol="application/pgp-signature"; boundary="===============8859708513165695336==" Message-Id: <[email protected]> Date: Tue, 04 Aug 2026 09:04:19 +0000 --===============8859708513165695336== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Source: picard-tools Source-Version: 3.5.0+dfsg-1 Done: Pierre Gruet <[email protected]> We believe that the bug you reported is fixed in the latest version of picard-tools, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet <[email protected]> (supplier of updated picard-tools package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 04 Aug 2026 10:35:16 +0200 Source: picard-tools Architecture: source Version: 3.5.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]= an.org> Changed-By: Pierre Gruet <[email protected]> Closes: 1139484 Changes: picard-tools (3.5.0+dfsg-1) unstable; urgency=3Dmedium . * New upstream version 3.5.0+dfsg: - This solves the FTBFS consecutive to the use of htsjdk 5.x (Closes: #1139484) * Refreshing patches * Raising Standards version to 4.7.4 (no change) * Replacing deprecated skip-non-installable autopkgtest restriction with t= he list of Architectures * Fixing type mismatches in tests . [ Andreas Tille ] * Remove myself from Uploaders Checksums-Sha1: 537fe1871828e9d12185d1663496329412703dd5 2720 picard-tools_3.5.0+dfsg-1.dsc 19633a82bba3eea0f580ec3d93363142f75121ca 59300696 picard-tools_3.5.0+dfsg.or= ig.tar.xz cfc75507d6ab7f7d8270e16d18b8d78841bb3b58 29236 picard-tools_3.5.0+dfsg-1.deb= ian.tar.xz 51f25ae664781cda42c1c28e511bab0cc2e06cea 19383 picard-tools_3.5.0+dfsg-1_amd= 64.buildinfo Checksums-Sha256: bf723067e4872786876522bd99c43ffdaa10a8585867085cf07a8359f4dc213f 2720 picard= -tools_3.5.0+dfsg-1.dsc 2a286a027b7a0a27015ee4adbe9c255e6695baed8eb6180896e6736c81548738 59300696 pi= card-tools_3.5.0+dfsg.orig.tar.xz e3fb215e57a0c5dd1df00b699b43cf23059ecd3aa69a7104233a1bf4ad06c776 29236 picar= d-tools_3.5.0+dfsg-1.debian.tar.xz cd0000fe086cab7da840c9c5b80e5a2d54e40da6ca9d7e0d1764891416cc0bae 19383 picar= d-tools_3.5.0+dfsg-1_amd64.buildinfo Files: 56f7d55c75c0625b64bb3017c4aba801 2720 science optional picard-tools_3.5.0+df= sg-1.dsc 3b2edb61a3adaec6ae13535dfcd7e29b 59300696 science optional picard-tools_3.5.= 0+dfsg.orig.tar.xz 15a0e8c19c78c2ae1577cbb39c84dc99 29236 science optional picard-tools_3.5.0+d= fsg-1.debian.tar.xz 157978451c990be2fa0cb0d1eeb028d0 19383 science optional picard-tools_3.5.0+d= fsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmpxptsACgkQYAMWptwn dHYjfA/+Mx/I8/ZZIaUhQcmzyzMTw7djk6gZIo67SRPUARG4GRKtpnFrMojK1OZm 6xfg/77p1UyhRaCTbwgg8HIt7jyzmnR9tBUQW32ccJSBrTlZZFT13H2Ka5/Fsu0C L+0VomHfh10AFvxVFUagLR6pKh+2g+StuZ/ZVHokk3UD1p59RSVMHuVw3eQNkiSj 9gkwAov/Mad+fJtnmmlkrcL8Ri3k71xI07hzzrN6LwNiMbFqOfXJeUGLCdRSkQtp xe8VcglMe033qxZ3AtE0Y9SNyABwzXTsV8njb0e1EScHxm+l73MuRIq5JooLRsyG 8kalY9rxBe5AdfejLrcPQWRYQWao551mKfadeblhw0HELpFY/CKJCKkgfAbOwl0F BQzO1i+hnmHpSWdoHP8byOC68RAF08pUPwaPIELu7LYSy4DiErRnp0x5V/d08ylO F8zU8A4nfWpzU8T6YR6vWcX1PU4ZH5dI+U592wDrCTajj6xXsN5Tki7w5Z++53Uu r59kbupUFDa6YitP3DjiS2wlD1to2dKNNWruEIgLHoId/U/pSG73S0nqhX5jx6oI RZtCG1c57n8xlm/qkcEBve4+TfVAZS93FcB1C0RvjkAQVwLLrqch4pbR4ez+ZYiS tyyYIR0GOaT/02sozU+yuvy99VMEhS0w/Xdt+ah2s2YeASA8pEs=3D =3DcdGU -----END PGP SIGNATURE----- --===============8859708513165695336== Content-Type: application/pgp-signature -----BEGIN PGP SIGNATURE----- iHUEABYIAB0WIQTziqJOuF8J+ZI8pJSb9qggYcy5IQUCanGrEwAKCRCb9qggYcy5 IYKFAQDP5tcfVU8C+caSKSdVicutVSVpk24unB6HJohQO2yksgD/cGb19Zebf9Cm JoLuEAIcrqieKGh4BXmeJK2zTeGZMww= =3VCf -----END PGP SIGNATURE----- --===============8859708513165695336==-- ------------=_1785834427-3318911-0--