Your message dated Sun, 29 Mar 2026 19:48:52 +0000
with message-id <[email protected]>
and subject line Bug#1108566: fixed in gradle 4.4.1-23
has caused the Debian Bug report #1108566,
regarding 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
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.)
--
1108566: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108566
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: gradle
Source-Version: 4.4.1-23
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
gradle, 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 gradle 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: Sun, 29 Mar 2026 21:17:21 +0200
Source: gradle
Architecture: source
Version: 4.4.1-23
Distribution: unstable
Urgency: medium
Maintainer: Debian Java Maintainers
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1108566
Changes:
gradle (4.4.1-23) unstable; urgency=medium
.
* Team upload
* Raising Standards version to 4.7.3:
- Removing Priority: optional, which is default
* Rewriting d/watch with version 5
* Fixing old FSF address in d/copyright
.
[ Vladimir Petko ]
* d/p/java25-compat.patch: catch exception when clearing
Security Manager (Closes: #1108566).
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Files:
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