[Debian-med-packaging] Bug#1096676: gatk-bwamem: ftbfs with GCC-15

Mon Feb 17 17:14:46 GMT 2025

Package: src:gatk-bwamem
Version: 1.0.4+dfsg2-3
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
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