Control: tags -1 pending This issue should be fixed in https://salsa.debian.org/med-team/picard-tools/commit/4da851972983cee93a3cce27bfbb40f9648dcc3d
While fixing the bug I also tried to upgrade the package to the latest upstream version. Unfortunately this failed with: Compiling build file '/build/picard-tools-2.18.14+dfsg/build.gradle' using BuildScriptTransformer. Adding Maven pom generation to project 'picard' Linking the generated javadoc to the system JDK API documentation FAILURE: Build failed with an exception. * Where: Build file '/build/picard-tools-2.18.14+dfsg/build.gradle' line: 53 * What went wrong: A problem occurred evaluating root project 'picard'. > The ClassLoader obtained from the Java ToolProvider is null. A Java 8 JDK > must be installed. See > https://github.com/broadinstitute/picard/blob/master/README.md#building-picard > for information on how to build picard * Try: Run with --debug option to get more log output. * Exception is: org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'picard'. 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$1.run(StoppableExecutorImpl.java:46) Caused by: org.gradle.api.GradleException: The ClassLoader obtained from the Java ToolProvider is null. A Java 8 JDK must be installed. See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at build_e2g2wljk0xfne1q452c0qhi2d.ensureBuildPrerequisites(/build/picard-tools-2.18.14+dfsg/build.gradle:53) at build_e2g2wljk0xfne1q452c0qhi2d$ensureBuildPrerequisites.callCurrent(Unknown Source) at build_e2g2wljk0xfne1q452c0qhi2d.run(/build/picard-tools-2.18.14+dfsg/build.gradle:61) at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90) ... 62 more BUILD FAILED Total time: 6.725 secs Could any of the more skilled Java developers of the team please have a look? Kind regards Andreas. -- http://fam-tille.de