Bug#1026757: gatk-native-bindings: FTBFS: make[1]: *** [debian/rules:13: override_dh_auto_build] Error 25
Lucas Nussbaum
lucas at debian.org
Tue Dec 20 17:31:38 GMT 2022
Source: gatk-native-bindings
Version: 1.0.0-2.1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20221220 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_build -- jar
> 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=gatk-native-bindings -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar
> OpenJDK 64-Bit Server VM warning: Ignoring option --illegal-access=permit; support was removed in 17.0
> Initialized native services in: /<<PKGBUILDDIR>>/.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: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 1.208 secs.
> The client will now receive all logging from the daemon (pid: 1153077). The daemon log file: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1/daemon-1153077.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 8 worker leases.
> Creating new cache for fileHashes, path /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 1ec3cd8a
> Creating new cache for resourceHashesCache, path /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at 1ec3cd8a
> Creating new cache for fileHashes, path /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 27eb4497
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Could not create service of type ScriptPluginFactory using BuildScopeServices.createScriptPluginFactory().
> > Could not create service of type PluginResolutionStrategyInternal using BuildScopeServices.createPluginResolutionStrategy().
>
> * Try:
> Run with --debug option to get more log output. Run with --scan to get full insights.
>
> * Exception is:
> org.gradle.internal.service.ServiceCreationException: Could not create service of type ScriptPluginFactory using BuildScopeServices.createScriptPluginFactory().
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryMethodService.invokeMethod(DefaultServiceRegistry.java:797)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.create(DefaultServiceRegistry.java:748)
> at org.gradle.internal.service.DefaultServiceRegistry$ManagedObjectProvider.getInstance(DefaultServiceRegistry.java:574)
> at org.gradle.internal.service.DefaultServiceRegistry$SingletonService.get(DefaultServiceRegistry.java:623)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.assembleParameters(DefaultServiceRegistry.java:761)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.create(DefaultServiceRegistry.java:747)
> at org.gradle.internal.service.DefaultServiceRegistry$ManagedObjectProvider.getInstance(DefaultServiceRegistry.java:574)
> at org.gradle.internal.service.DefaultServiceRegistry$SingletonService.get(DefaultServiceRegistry.java:623)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.assembleParameters(DefaultServiceRegistry.java:761)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.create(DefaultServiceRegistry.java:747)
> at org.gradle.internal.service.DefaultServiceRegistry$ManagedObjectProvider.getInstance(DefaultServiceRegistry.java:574)
> at org.gradle.internal.service.DefaultServiceRegistry$SingletonService.get(DefaultServiceRegistry.java:623)
> at org.gradle.internal.service.DefaultServiceRegistry.doGet(DefaultServiceRegistry.java:344)
> at org.gradle.internal.service.DefaultServiceRegistry.get(DefaultServiceRegistry.java:325)
> at org.gradle.initialization.DefaultGradleLauncherFactory.doNewInstance(DefaultGradleLauncherFactory.java:174)
> at org.gradle.initialization.DefaultGradleLauncherFactory.newInstance(DefaultGradleLauncherFactory.java:106)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:40)
> 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.internal.service.ServiceCreationException: Could not create service of type PluginResolutionStrategyInternal using BuildScopeServices.createPluginResolutionStrategy().
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryMethodService.invokeMethod(DefaultServiceRegistry.java:797)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.create(DefaultServiceRegistry.java:748)
> at org.gradle.internal.service.DefaultServiceRegistry$ManagedObjectProvider.getInstance(DefaultServiceRegistry.java:574)
> at org.gradle.internal.service.DefaultServiceRegistry$SingletonService.get(DefaultServiceRegistry.java:623)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.assembleParameters(DefaultServiceRegistry.java:761)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryService.create(DefaultServiceRegistry.java:747)
> at org.gradle.internal.service.DefaultServiceRegistry$ManagedObjectProvider.getInstance(DefaultServiceRegistry.java:574)
> at org.gradle.internal.service.DefaultServiceRegistry$SingletonService.get(DefaultServiceRegistry.java:623)
> at org.gradle.internal.service.DefaultServiceRegistry.doGet(DefaultServiceRegistry.java:344)
> at org.gradle.internal.service.DefaultServiceRegistry.get(DefaultServiceRegistry.java:325)
> at org.gradle.internal.service.scopes.BuildScopeServices.defaultScriptPluginFactory(BuildScopeServices.java:300)
> at org.gradle.internal.service.scopes.BuildScopeServices.createScriptPluginFactory(BuildScopeServices.java:287)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
> at org.gradle.internal.service.ReflectionBasedServiceMethod.invoke(ReflectionBasedServiceMethod.java:35)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryMethodService.invokeMethod(DefaultServiceRegistry.java:795)
> ... 60 more
> Caused by: org.gradle.api.GradleException: Could not generate a proxy class for class org.gradle.plugin.management.internal.DefaultPluginResolutionStrategy.
> at org.gradle.api.internal.AbstractClassGenerator.generateUnderLock(AbstractClassGenerator.java:223)
> at org.gradle.api.internal.AbstractClassGenerator.generate(AbstractClassGenerator.java:79)
> at org.gradle.api.internal.ClassGeneratorBackedInstantiator.newInstance(ClassGeneratorBackedInstantiator.java:36)
> at org.gradle.plugin.internal.PluginUsePluginServiceRegistry$BuildScopeServices.createPluginResolutionStrategy(PluginUsePluginServiceRegistry.java:113)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
> at org.gradle.internal.service.ReflectionBasedServiceMethod.invoke(ReflectionBasedServiceMethod.java:35)
> at org.gradle.internal.service.DefaultServiceRegistry$FactoryMethodService.invokeMethod(DefaultServiceRegistry.java:795)
> ... 77 more
> Caused by: org.gradle.internal.UncheckedException: java.lang.IllegalAccessException: module java.base does not open java.lang to unnamed module @47faa49c
> at org.gradle.internal.UncheckedException.throwAsUncheckedException(UncheckedException.java:63)
> at org.gradle.internal.UncheckedException.throwAsUncheckedException(UncheckedException.java:40)
> at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:76)
> at org.gradle.internal.classloader.ClassLoaderUtils$LookupClassDefiner.defineClass(ClassLoaderUtils.java:142)
> at org.gradle.internal.classloader.ClassLoaderUtils.define(ClassLoaderUtils.java:92)
> at org.gradle.model.internal.asm.AsmClassGenerator.define(AsmClassGenerator.java:58)
> at org.gradle.model.internal.asm.AsmClassGenerator.define(AsmClassGenerator.java:54)
> at org.gradle.api.internal.AsmBackedClassGenerator$ClassBuilderImpl.generate(AsmBackedClassGenerator.java:967)
> at org.gradle.api.internal.AbstractClassGenerator.generateUnderLock(AbstractClassGenerator.java:221)
> ... 86 more
> Caused by: java.lang.IllegalAccessException: module java.base does not open java.lang to unnamed module @47faa49c
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
> ... 92 more
>
>
> * Get more help at https://help.gradle.org
>
> BUILD FAILED in 2s
> 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=gatk-native-bindings -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar returned exit code 1
> make[1]: *** [debian/rules:13: override_dh_auto_build] Error 25
The full build log is available from:
http://qa-logs.debian.net/2022/12/20/gatk-native-bindings_1.0.0-2.1_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221220;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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