Re: [Debian-med-packaging] Problems building latest version of htsjdk
On 09/17/2018 04:41 PM, Andreas Tille wrote:
> Hi
>
> should I write "as usual" I have problems to upgrade the latest version
> of htsjdk. I've injected the latest version in Git but I get:
Hi,
I can't find any git update on salsa for htsjdk (last update 1 month
ago), forgot to push?
Olivier
>
>
> ...
> FAILURE: Build failed with an exception.
>
> * Where:
> Build file '/build/htsjdk-2.16.1+dfsg/build.gradle' line: 107
>
> * What went wrong:
> A problem occurred evaluating root project 'htsjdk'.
>> Could not find method tags() for arguments [build_7yzoudgavx97ss85wjypy0wdo$_run_closure7$_closure20@6f808ba4] on task ':testFTP' of type org.gradle.api.tasks.testing.Test.
> * Try:
> Run with --debug option to get more log output.
>
> * Exception is:
> org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'htsjdk'.
> at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92)
> at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)
> at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)
> at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)
> at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:39)
> at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
> at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:70)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
> at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
> at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
> at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
> at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:599)
> at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125)
> at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
> at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
> at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
> at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:233)
> at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:230)
> at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:56)
> at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:160)
> at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:119)
> at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:102)
> at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:71)
> at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
> at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
> at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
> at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
> at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:49)
> at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:31)
> 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:120)
> at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
> at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
> FAILURE: Build failed with an exception.
>
> * Where:
> Build file '/build/htsjdk-2.16.1+dfsg/build.gradle' line: 107
>
> * What went wrong:
> A problem occurred evaluating root project 'htsjdk'.
>> Could not find method tags() for arguments [build_7yzoudgavx97ss85wjypy0wdo$_run_closure7$_closure20@6f808ba4] on task ':testFTP' of type org.gradle.api.tasks.testing.Test.
> * Try:
> Run with --debug option to get more log output.
>
> * Exception is:
> org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'htsjdk'.
> at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92)
> at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)
> at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)
> at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)
> at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:39)
> at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
> at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:70)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
> at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
> at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
> at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
> at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:599)
> at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125)
> at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
> at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
> at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
> at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:233)
> at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:230)
> at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:56)
> at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:160)
> at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:119)
> at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:102)
> at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:71)
> at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
> at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
> at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
> at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
> at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:49)
> at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:31)
> 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:120)
> at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> 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:120)
> at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:60)
> at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
> at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
> at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
> at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
> at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:46)
> Caused by: org.gradle.internal.metaobject.AbstractDynamicObject$CustomMessageMissingMethodException: Could not find method tags() for arguments [build_7yzoudgavx97ss85wjypy0wdo$_run_closure7$_closure20@6f808ba4] on task ':testFTP' of type org.gradle.api.tasks.testing.Test.
> at org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)
> at org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)
> at build_7yzoudgavx97ss85wjypy0wdo$_run_closure7.doCall(/build/htsjdk-2.16.1+dfsg/build.gradle:107)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at org.gradle.api.internal.ClosureBackedAction.execute(ClosureBackedAction.java:70)
> at org.gradle.util.ConfigureUtil.configureTarget(ConfigureUtil.java:160)
> at org.gradle.util.ConfigureUtil.configureSelf(ConfigureUtil.java:136)
> at org.gradle.api.internal.AbstractTask.configure(AbstractTask.java:528)
> at org.gradle.api.internal.project.DefaultProject.task(DefaultProject.java:1015)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at org.gradle.internal.metaobject.BeanDynamicObject$MetaClassAdapter.invokeMethod(BeanDynamicObject.java:464)
> at org.gradle.internal.metaobject.BeanDynamicObject.invokeMethod(BeanDynamicObject.java:176)
> at org.gradle.internal.metaobject.CompositeDynamicObject.invokeMethod(CompositeDynamicObject.java:96)
> at org.gradle.internal.metaobject.MixInClosurePropertiesAsMethodsDynamicObject.invokeMethod(MixInClosurePropertiesAsMethodsDynamicObject.java:30)
> at org.gradle.groovy.scripts.BasicScript.invokeMethod(BasicScript.java:111)
> at org.gradle.groovy.scripts.BasicScript.methodMissing(BasicScript.java:120)
> 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 build_7yzoudgavx97ss85wjypy0wdo.run(/build/htsjdk-2.16.1+dfsg/build.gradle:105)
> at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)
> ... 62 more
>
>
> BUILD FAILED
>
> Total time: 6.232 secs
>
>
> Any help would be welcome
>
> Andreas.
>
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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