Java error while installing picard using gradlew

Dear all, I am trying to install picard in my Ubuntu 16.04 Virtual Machine. I cloned the repo and then I used gradlew to install the package. But it failed because of a java error:

stefania@stefania-VirtualBox:~/picard$ ./gradlew shadowJar
FAILURE: Build failed with an exception.
* Where:
Build file '/home/stefania/picard/build.gradle' line: 56
* What went wrong:
A problem occurred evaluating root project 'picard'.
> Cannot cast object 'jdk.internal.loader.ClassLoaders$AppClassLoader@c39f790' with class 'jdk.internal.loader.ClassLoaders$AppClassLoader' to class 'java.net.URLClassLoader'
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
BUILD FAILED
Total time: 9.328 secs

* 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:38) at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:25) at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34) at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:55) at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:573) at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125) at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:42) at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38) at org.gradle.initialization.DefaultGradleLauncher$2.run(DefaultGradleLauncher.java:151) at org.gradle.internal.Factories$1.create(Factories.java:22) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:53) at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:148) at org.gradle.initialization.DefaultGradleLauncher.access$200(DefaultGradleLauncher.java:33) at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:112) at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:106) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:63) at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:106) at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:92) at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:66) 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:79) at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:51) at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:59) 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:55) 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.HintGCAfterBuild.execute(HintGCAfterBuild.java:44) 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$1.run(DaemonStateCoordinator.java:293) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54) at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40) Caused by: org.codehaus.groovy.runtime.typehandling.GroovyCastException: Cannot cast object 'jdk.internal.loader.ClassLoaders$AppClassLoader@c39f790' with class 'jdk.internal.loader.ClassLoaders$AppClassLoader' to class 'java.net.URLClassLoader' at build_an5ohpitbsvmbx43zaazp4yd.run(/home/stefania/picard/build.gradle:56) at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90) ... 58 more

My java version is: openjdk version “9-internal” OpenJDK Runtime Environment (build 9-internal+0-2016-04-14-195246.buildd.src) OpenJDK 64-Bit Server VM (build 9-internal+0-2016-04-14-195246.buildd.src, mixed mode)

I googled the error but I didn’t find anything useful. Can you please help me in solving the issue?

Thanks in advance!

[smerella]

Great! It works now!! I downgraded to java 8:

sudo apt-get remove --purge openjdk*
sudo add-apt-repository -y ppa:webupd8team/java
sudo apt-get update
sudo apt-get -y install oracle-java8-installer

Then I re-run the command and the now I have BUILD SUCCESSFUL 😃

Many many thanks!!!

[cmnbroad]

Oh, it sounds like maybe you’re trying to build picard (from the github repo ?) rather than just install it ? If so, you need to install a JDK, not just a Java runtime. Are you running a gradle command ? If you post the actual command line you’re running, and the error output from the command line, we could probably help get you back on the right path.