Your message dated Sat, 13 Dec 2025 14:36:52 +0000
with message-id <[email protected]>
and subject line Bug#1096676: fixed in gatk-bwamem 1.0.4+dfsg3-1
has caused the Debian Bug report #1096676,
regarding gatk-bwamem: ftbfs with GCC-15
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
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--
1096676: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096676
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:gatk-bwamem
Version: 1.0.4+dfsg2-3
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/gatk-bwamem_1.0.4+dfsg2-3_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other Common build failures are new warnings resulting in build failures
with -Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-15/porting_to.html
[...]
:test (Thread[#48,Task worker for ':' Thread 2,5,main]) completed. Took 1.036
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 134
* 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 134
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:103)
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 6s
5 actionable tasks: 3 executed, 2 up-to-date
dh_auto_test: error: gradle --info --console plain --offline --stacktrace
--no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=.
-Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8
--parallel --max-workers=8 test returned exit code 1
make[1]: *** [debian/rules:45: override_dh_auto_test] Error 25
make[1]: Leaving directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2'
make: *** [debian/rules:16: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: gatk-bwamem
Source-Version: 1.0.4+dfsg3-1
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
gatk-bwamem, 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 gatk-bwamem 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: Sat, 13 Dec 2025 15:00:25 +0100
Source: gatk-bwamem
Architecture: source
Version: 1.0.4+dfsg3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1096676
Changes:
gatk-bwamem (1.0.4+dfsg3-1) unstable; urgency=medium
.
* New upstream version 1.0.4+dfsg3:
- Only the bwa part was updated
* Refreshing patches
* Raising Standards version to 4.7.2 (no change)
* Adding a --debug flag to circumvent problem with gradle output
Closes: #1096676
* Fixing syntax in header of patch for freebsd
* Rewriting d/watch with version 5
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