[From nobody Sun Mar 29 20:51:06 2026 Received: (at submit) by bugs.debian.org; 22 Mar 2026 18:23:44 +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=-120.7 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,HAS_PACKAGE,MONEY, SPF_HELO_PASS,SPF_NONE,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, 127; hammy, 150; neutral, 632; spammy, 0. spammytokens: hammytokens:0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--H*F:U*sanvila, 0.000-+--H*rp:U*sanvila, 0.000-+--sk:dh_auto Return-path: <sanvila@debian.org> Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72]:51150) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1w4NSh-00AzVR-30 for submit@bugs.debian.org; Sun, 22 Mar 2026 18:23:44 +0000 Received: via submission from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=paradis.debian.org, EMAIL=hostmaster@paradis.debian.org (verified) by mailly.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1w4NSg-00CoJb-1C for submit@bugs.debian.org; Sun, 22 Mar 2026 18:23:42 +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=rEdSzrMh1jllI+VkWE1/8e86x+G3pk8yuGYt7kmRHBU=; b=VkKbo4KJ9183+ORctz5m+JJJOk KTIgGwALbv/cYPKSgEMqhG0Gqy4urOYGBEDxS0yQVtc8uQ/SzQ2lQ+MZAQVr7YIML1okQKcWkiDYn SuWLUQABSVkHAaw74VoqkfO2PzcMMmVoUN4dYmwdJQKshAdf0R4AQgYnzaEHCa2A354Ir7a1soA/Z W+XpLIn/FqUA2eptSNsvDUYqf0mWVwAGJdHwZNta//NgHACOTMQE+GLOIxg2wh5iHNO93qmqnFl0n yTyedaRo7X/+9EiyVO8/qPAJilTb5fxwZ8ge3PO/FgIClHD10Z5w4phIJ20skvC0CT+msVDBxgzhR WdfUY/Iw==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1w4NSf-00Fxzx-0F for submit@bugs.debian.org; Sun, 22 Mar 2026 18:23:41 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> 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: sanvila@debian.org Message-Id: <E1w4NSf-00Fxzx-0F@paradis.debian.org> Date: Sun, 22 Mar 2026 18:23:41 +0000 Delivered-To: submit@bugs.debian.org 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/202603/ 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 "unlink|u" 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 ...] Running Test: Test method testWgsMetricsMerge[6](GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 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 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 2 SD_COVERAGE 0 MEDIAN_COVERAGE 2 MAD_COVERAGE 0 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 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 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 )(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. java.lang.UnsupportedOperationException: Setting a Security Manager is not supported at java.base/java.lang.System.setSecurityManager(System.java:304) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:76) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:44) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:83) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:35) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:119) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:64) at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:62) at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:67) Results: SUCCESS (5255 tests, 5255 successes, 0 failures, 0 skipped) :test FAILED :test (Thread[#48,Task worker for ':',5,main]) completed. Took 5 mins 56.992 secs. FAILURE: Build failed with an exception. * What went wrong: Execution failed for task ':test'. > Process 'Gradle Test Executor 1' finished with non-zero exit value 1 * 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.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.process.internal.ExecException: Process 'Gradle Test Executor 1' finished with non-zero exit value 1 at org.gradle.process.internal.DefaultExecHandle$ExecResultImpl.assertNormalExitValue(DefaultExecHandle.java:382) at org.gradle.process.internal.worker.DefaultWorkerProcess.waitForStop(DefaultWorkerProcess.java:190) at org.gradle.process.internal.worker.DefaultWorkerProcessBuilder$MemoryRequestingWorkerProcess.waitForStop(DefaultWorkerProcessBuilder.java:228) at org.gradle.api.internal.tasks.testing.worker.ForkingTestClassProcessor.stop(ForkingTestClassProcessor.java:122) at org.gradle.api.internal.tasks.testing.processors.RestartEveryNTestClassProcessor.endBatch(RestartEveryNTestClassProcessor.java:63) at org.gradle.api.internal.tasks.testing.processors.RestartEveryNTestClassProcessor.stop(RestartEveryNTestClassProcessor.java:57) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.FailureHandlingDispatch.dispatch(FailureHandlingDispatch.java:29) at org.gradle.internal.dispatch.AsyncDispatch.dispatchMessages(AsyncDispatch.java:133) at org.gradle.internal.dispatch.AsyncDispatch.access$000(AsyncDispatch.java:34) at org.gradle.internal.dispatch.AsyncDispatch$1.run(AsyncDispatch.java:73) at org.gradle.internal.operations.BuildOperationIdentifierPreservingRunnable.run(BuildOperationIdentifierPreservingRunnable.java:39) ... 3 more * Get more help at https://help.gradle.org BUILD FAILED in 6m 7s 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 -------------------------------------------------------------------------------- ]