SonarQube 6.0 analysis fails on module without code

ENVIRONMENT

Jenkins 2.23
SonarQube plugin 2.4.4
SonarQube 6.0
Java plugin 4.2
Findbugs plugin 3.4.3
Clirr 1.3
(some other plugins, probably not relevant for this issue, but feel free to ask in the comments and I´ll edit the question)

I have a multi-module Maven project with one root module (pom packaging, no code) and several child modules (jar packaging, code). I´m running SonarQube analysis in a Maven job in Jenkins.

PROBLEM DESCRIPTION

Analysis worked ok in SQ 5.x. Since upgrading to SQ 6.0, the analysis fails:

the analysis on the child modules succeeds
the analysis on the root module fails with error:

[ERROR] Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.6:sonar (default-cli) on project root: org.sonar.plugins.java.api.JavaResourceLocator.findResourceByClassName(Ljava/lang/String;)Lorg/sonar/api/resources/Resource; -> [Help 1]

ALREADY TRIED

excluding the root module from analysis --> results in Maven error

Unable to determine structure of project. Probably you use Maven Advanced Reactor Options with a broken tree of modules. "foo" is orphan

Findbugs plugin 3.4.4 from https://github.com/SonarQubeCommunity/sonar-findbugs/releases (as hinted in API incompatibility with SonarQube 5.6 and Java Analyzer 4.0 with Findbugs 3.3 or Cobertura 1.6.3) --> same error

DEBUG LOGGING

Maven with -e and -X

[ERROR] Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.6:sonar (default-cli) on project root: org.sonar.plugins.java.api.JavaResourceLocator.findResourceByClassName(Ljava/lang/String;)Lorg/sonar/api/resources/Resource; -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.6:sonar (default-cli) on project root: org.sonar.plugins.java.api.JavaResourceLocator.findResourceByClassName(Ljava/lang/String;)Lorg/sonar/api/resources/Resource;
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
    at org.jvnet.hudson.maven3.launcher.Maven32Launcher.main(Maven32Launcher.java:132)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:330)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:238)
    at jenkins.maven3.agent.Maven32Main.launch(Maven32Main.java:186)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at hudson.maven.Maven3Builder.call(Maven3Builder.java:136)
    at hudson.maven.Maven3Builder.call(Maven3Builder.java:71)
    at hudson.remoting.UserRequest.perform(UserRequest.java:153)
    at hudson.remoting.UserRequest.perform(UserRequest.java:50)
    at hudson.remoting.Request$2.run(Request.java:332)
    at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.maven.plugin.MojoExecutionException: org.sonar.plugins.java.api.JavaResourceLocator.findResourceByClassName(Ljava/lang/String;)Lorg/sonar/api/resources/Resource;
    at org.codehaus.mojo.sonar.bootstrap.ExceptionHandling.handle(ExceptionHandling.java:41)
    at org.codehaus.mojo.sonar.bootstrap.RunnerBootstraper.execute(RunnerBootstraper.java:139)
    at org.codehaus.mojo.sonar.SonarMojo.execute(SonarMojo.java:132)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
    ... 31 more
Caused by: java.lang.NoSuchMethodError: org.sonar.plugins.java.api.JavaResourceLocator.findResourceByClassName(Ljava/lang/String;)Lorg/sonar/api/resources/Resource;
    at org.sonar.plugins.clirr.ClirrSensor.saveIssues(ClirrSensor.java:94)
    at org.sonar.plugins.clirr.ClirrSensor.analyse(ClirrSensor.java:76)
    at org.sonar.scanner.phases.SensorsExecutor.executeSensor(SensorsExecutor.java:57)
    at org.sonar.scanner.phases.SensorsExecutor.execute(SensorsExecutor.java:49)
    at org.sonar.scanner.phases.AbstractPhaseExecutor.execute(AbstractPhaseExecutor.java:78)
    at org.sonar.scanner.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:184)
    at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:142)
    at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:127)
    at org.sonar.scanner.scan.ProjectScanContainer.scan(ProjectScanContainer.java:241)
    at org.sonar.scanner.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:236)
    at org.sonar.scanner.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:234)
    at org.sonar.scanner.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:226)
    at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:142)
    at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:127)
    at org.sonar.scanner.task.ScanTask.execute(ScanTask.java:47)
    at org.sonar.scanner.task.TaskContainer.doAfterStart(TaskContainer.java:86)
    at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:142)
    at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:127)
    at org.sonar.scanner.bootstrap.GlobalContainer.executeTask(GlobalContainer.java:115)
    at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:118)
    at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:78)
    at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:48)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:87)
    at org.sonar.runner.impl.BatchLauncher$1.run(BatchLauncher.java:75)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.sonar.runner.impl.BatchLauncher.doExecute(BatchLauncher.java:69)
    at org.sonar.runner.impl.BatchLauncher.execute(BatchLauncher.java:50)
    at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:102)
    at org.sonar.runner.api.Runner.execute(Runner.java:100)
    at org.codehaus.mojo.sonar.bootstrap.RunnerBootstraper.execute(RunnerBootstraper.java:135)
    ... 34 more
[ERROR] 
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

QUESTION

Is this a configuration issue at my end? Or is there an issue with SonarQube or any of the plugins?

I will also accept answers that let me exclude the codeless root module as a workaround, without any interference for the child modules that have it as a parent.

Solution

The lines that might have raised your attention are the following ones:

Caused by: java.lang.NoSuchMethodError: org.sonar.plugins.java.api.JavaResourceLocator.findResourceByClassName(Ljava/lang/String;)Lorg/sonar/api/resources/Resource;
    at org.sonar.plugins.clirr.ClirrSensor.saveIssues(ClirrSensor.java:94)

You must uninstall the Clirr plugin: it is not compatible with SonarQube 6.0.