[Debian-med-packaging] Bug#974076: igv: FTBFS error: module not found: junit4
Andreas Beckmann
anbe at debian.org
Mon Nov 9 16:59:03 GMT 2020
Package: igv
Version: 2.6.3+dfsg-1
Severity: serious
Tags: ftbfs
Justification: fails to build from source
Hi,
igv recently started to FTBFS, this is probably caused by a change in some build-dependency:
dh_auto_test -O--buildsystem=gradle
mkdir -p .gradle/init.d
cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=3 test
Initialized native services in: /build/igv-2.6.3+dfsg/.gradle/native
To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html.
Starting process 'Gradle build daemon'. Working directory: /build/igv-2.6.3+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.en
coding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 0.496 secs.
The client will now receive all logging from the daemon (pid: 18018). The daemon log file: /build/igv-2.6.3+dfsg/.gradle/daemon/4.4.1/daemon-18018.out.log
Daemon will be stopped at the end of the build stopping after processing
Closing daemon's stdin at end of input.
The daemon will no longer process any standard input.
Using 3 worker leases.
Creating new cache for fileHashes, path /build/igv-2.6.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 675abdc5
Creating new cache for resourceHashesCache, path /build/igv-2.6.3+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at 675abdc5
Creating new cache for fileHashes, path /build/igv-2.6.3+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 42ea24b0
Starting Build
Creating new cache for metadata-1.1/results, path /build/igv-2.6.3+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess at 521692c9
Settings evaluated using settings file '/build/igv-2.6.3+dfsg/settings.gradle'.
Projects loaded. Root project using build file '/build/igv-2.6.3+dfsg/build.gradle'.
Included projects: [root project 'igv']
Keep-alive timer started
Adding Debian repository to project 'igv'
Parallel execution is an incubating feature.
Evaluating root project 'igv' using build file '/build/igv-2.6.3+dfsg/build.gradle'.
Adding Maven pom generation to project 'igv'
Linking the generated javadoc to the system JDK API documentation
All projects evaluated.
Selected primary task 'test' from project :
Creating new cache for annotation-processors, path /build/igv-2.6.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess at 11b080fd
Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test']
Creating new cache for resourceHashesCache, path /build/igv-2.6.3+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at 42ea24b0
Creating new cache for taskHistory, path /build/igv-2.6.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess at 6937ae2c
Creating new cache for outputFiles, path /build/igv-2.6.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess at 2b1f6e31
:compileJava (Thread[Daemon worker,5,main]) started.
:compileJava
Putting task artifact state for task ':compileJava' into context took 0.003 secs.
Loading the Maven rules...
Passing through org.apache.logging.log4j:log4j-api:jar:debian
Passing through org.apache.logging.log4j:log4j:jar:debian
Skipping task ':compileJava' as it is up-to-date (took 0.49 secs).
:compileJava UP-TO-DATE
:compileJava (Thread[Daemon worker,5,main]) completed. Took 0.517 secs.
:processResources (Thread[Daemon worker,5,main]) started.
:processResources
Putting task artifact state for task ':processResources' into context took 0.0 secs.
Skipping task ':processResources' as it is up-to-date (took 0.052 secs).
:processResources UP-TO-DATE
:processResources (Thread[Daemon worker,5,main]) completed. Took 0.054 secs.
:classes (Thread[Daemon worker,5,main]) started.
:classes
Skipping task ':classes' as it has no actions.
:classes UP-TO-DATE
:classes (Thread[Daemon worker,5,main]) completed. Took 0.0 secs.
:compileTestJava (Thread[Daemon worker,5,main]) started.
:compileTestJava
Putting task artifact state for task ':compileTestJava' into context took 0.0 secs.
Up-to-date check for task ':compileTestJava' took 0.778 secs. It is not up-to-date because:
No history is available.
All input files are considered out-of-date for incremental task ':compileTestJava'.
Compiling with JDK Java compiler API.
error: module not found: junit4
1 error
:compileTestJava FAILED
:compileTestJava (Thread[Daemon worker,5,main]) completed. Took 1.319 secs.
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':compileTestJava'.
> Compilation failed; see the compiler error output for details.
* 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 ':compileTestJava'.
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.internal.tasks.compile.CompilationFailedException: Compilation failed; see the compiler error output for details.
at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:50)
at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:35)
at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:98)
at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:51)
at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37)
at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
at org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:207)
at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:192)
at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:124)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
at org.gradle.api.internal.project.taskfactory.IncrementalTaskAction.doExecute(IncrementalTaskAction.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.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 4s
3 actionable tasks: 1 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=igv -Dfile.encoding=UTF-8 --parallel --max-workers=3 test returned exit code 1
make: *** [debian/rules:9: binary] Error 25
Andreas
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