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MojoExecutionException when building Geoserver with maven

I am trying to build GeoServer from source code. I got the following error when attempting to run a maven command from 'geoserver/src'.
[ERROR] Failed to execute goal pl.project13.maven:git-commit-id-plugin:2.1.15:revision (default) on project geoserver: Could not complete Mojo execution... Unable to find commits until some tag: Walk failure. Missing commit b3af7f46250c529c51402d2eb948987385690d3d -> [Help 1]
I tried to solve it with setting a proxy but failed. Anyone can help me out?Thanks in advance.
PS: here's the full stack trace of errors when I run mvn -X clean install
[ERROR] Failed to execute goal pl.project13.maven:git-commit-id-plugin:2.1.15:revision (default) on project geoserver: Could not complete Mojo execution... Unable to find commits until some tag: Walk failure. Missing commit b3af7f46250c529c51402d2eb948987385690d3d -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal pl.project13.maven:git-commit-id-plugin:2.1.15:revision (default) on project geoserver: Could not complete Mojo execution...
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.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Could not complete Mojo execution...
at pl.project13.maven.git.GitCommitIdMojo.handlePluginFailure(GitCommitIdMojo.java:457)
at pl.project13.maven.git.GitCommitIdMojo.execute(GitCommitIdMojo.java:393)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
... 20 more
Caused by: java.lang.RuntimeException: Unable to find commits until some tag
at pl.project13.jgit.JGitCommon.findCommitsUntilSomeTag(JGitCommon.java:286)
at pl.project13.jgit.DescribeCommand.call(DescribeCommand.java:298)
at pl.project13.maven.git.JGitProvider.getGitDescribe(JGitProvider.java:234)
at pl.project13.maven.git.JGitProvider.getGitDescribe(JGitProvider.java:125)
at pl.project13.maven.git.GitDataProvider.maybePutGitDescribe(GitDataProvider.java:139)
at pl.project13.maven.git.GitDataProvider.loadGitData(GitDataProvider.java:104)
at pl.project13.maven.git.GitCommitIdMojo.loadGitDataWithJGit(GitCommitIdMojo.java:585)
at pl.project13.maven.git.GitCommitIdMojo.loadGitData(GitCommitIdMojo.java:558)
at pl.project13.maven.git.GitCommitIdMojo.execute(GitCommitIdMojo.java:376)
... 22 more
Caused by: org.eclipse.jgit.errors.RevWalkException: Walk failure.
at org.eclipse.jgit.revwalk.RevWalk.iterator(RevWalk.java:1306)
at pl.project13.jgit.JGitCommon.findCommitsUntilSomeTag(JGitCommon.java:274)
... 30 more
Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing commit b3af7f46250c529c51402d2eb948987385690d3d
at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:149)
at org.eclipse.jgit.revwalk.RevWalk.getCachedBytes(RevWalk.java:884)
at org.eclipse.jgit.revwalk.RevCommit.parseHeaders(RevCommit.java:145)
at org.eclipse.jgit.revwalk.PendingGenerator.next(PendingGenerator.java:148)
at org.eclipse.jgit.revwalk.StartGenerator.next(StartGenerator.java:186)
at org.eclipse.jgit.revwalk.RevWalk.next(RevWalk.java:422)
at org.eclipse.jgit.revwalk.RevWalk.iterator(RevWalk.java:1304)
... 31 more
[ERROR]
[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

The reason of this trouble is that I are using a shallow clone of geoserver. Clone the entire repository will solve this issue.
Thanks for Mark Prins who answered my question at Geoserver-users mailing list

Building Hadoop on Windows 8.1. MojoException

I am trying to build Hadoop 2.7.3 on windows 8.1. There are numerous similar problems on stackoverflow but I could not solve the issue with the build I am trying. Following is the full stack trace after running the command with -e switch.
Failed to execute goal org.codehaus.mojo:exec-maven plugin:1.3.1:exec (compile-ms-winutils) on project hadoop-common: Command execution failed. Process exited with an error: 1 org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.3.1:exec (compile-ms-wi nutils) on project hadoop-common: Command execution failed. 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.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
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.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356) Caused by: org.apache.maven.plugin.MojoExecutionException: Command execution failed. at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:303)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
... 20 more Caused by: org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:402)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:164)
at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:750)
at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:292)
... 22 more
I am using SDK 8.1, maven 3.3.9, java 1.8, protoc 2.5.0, CMake 3.7, Git 2.10.2 and .net framework 4.5.1 with all the path variables properly set. I resolved some other issues during the process taking help form different posts here but badly stuck with this error message. Any help please?

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.

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.

To be honest, maybe this is not exactly the solution to your problem. But let me describe where I ran into a similar problem that matches your following description:
Unable to determine structure of project. Probably you use Maven Advanced Reactor Options with a broken tree of modules. "foo" is orphan.
I had changed my maven build to ci friendly as described by maven here.
Generally, my maven build was running fine until I added sonarqube check. Then I got the above-described message. It took a while to finde the problem and it was quite tricky.
By the way, I had a multiple module maven project running and the problem was that in my parent pom I was referring to the pom.xml instead of the folder.
<modules>
<module>modules/module1</module>
<!-- the reference to the pom.xml is the problem.
and will cause sonar to fail -->
<module>modules/module2/pom.xml</module>
</modules>

SonarQube 5.1 analysis fail with StackOverflowError

I recently upgraded to the newest SonarQube 5.1, but now, my maven builds have begun failing and I'm unable to determine what file is causing the error. The maven project is a multi module project.
SonarQube version 5.1
maven goal executed with "mvn sonar:sonar" (version 2.6 is used and the correctly analyses some of the projects)
The maven build finishes with the following error:
[ERROR] Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.6:sonar (default-cli) on project flex-parentpom: null: MojoExecutionException: StackOverflowError -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.6:sonar (default-cli) on project flex-parentpom: null
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:216)
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:120)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:347)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:154)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:584)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:213)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:157)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException
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:132)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
... 19 more
Caused by: java.lang.StackOverflowError
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.visitBinaryExpression(BaseTreeVisitor.java:208)
at org.sonar.java.model.expression.BinaryExpressionTreeImpl.accept(BinaryExpressionTreeImpl.java:85)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.scan(BaseTreeVisitor.java:42)
at org.sonar.java.resolve.SemanticModel$1.scan(SemanticModel.java:92)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.visitBinaryExpression(BaseTreeVisitor.java:208)
at org.sonar.java.model.expression.BinaryExpressionTreeImpl.accept(BinaryExpressionTreeImpl.java:85)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.scan(BaseTreeVisitor.java:42)
at org.sonar.java.resolve.SemanticModel$1.scan(SemanticModel.java:92)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.visitBinaryExpression(BaseTreeVisitor.java:208)
at org.sonar.java.model.expression.BinaryExpressionTreeImpl.accept(BinaryExpressionTreeImpl.java:85)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.scan(BaseTreeVisitor.java:42)
at org.sonar.java.resolve.SemanticModel$1.scan(SemanticModel.java:92)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.visitBinaryExpression(BaseTreeVisitor.java:208)
at org.sonar.java.model.expression.BinaryExpressionTreeImpl.accept(BinaryExpressionTreeImpl.java:85)
at org.sonar.plugins.java.api.tree.BaseTreeVisitor.scan(BaseTreeVisitor.java:42)
at org.sonar.java.resolve.SemanticModel$1.scan(SemanticModel.java:92)
Any ideas for debugging the cause of the error? I've attempted with -debug flag.

Problem solved.
I ended up setting up a local instance and running the maven plugin using a debugger, this allowed me to set a breakpoint at the exception. I turned out that we had a test case (file) which had a field defined by hundreds of Strings. This file has not been edited for a long time, so I guess the overall stack size has changed from 4.x to 5.x. The test was ugly and my solution in this case was therefore to refactor it. I guess another solution would be to increase the java stack size, but I've not tried it.

Sonarqube is not working after update

I updated SonarQube to 4.2 and it is not working at Jenkins now. T.T
Jenkins and SonarQube are installed in same server and I'm using mysql.
also, Jenkins setting for SonarQube is pointing the mysql db.
... and Maven version in Jenkins is 3.0.5
I don't set the sonar maven plugin in the java project.
It worked fine with Sonar 3.4.1 and I didn't change any setting on Jenkins after update the SonarQube.
here is error trace.
[ERROR] Expected one result (or null) to be returned by selectOne(), but found: 2
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 16.495s
[INFO] Finished at: Tue Apr 15 06:10:08 GMT 2014
[INFO] Final Memory: 20M/89M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.2:sonar (default-cli) on project java-utils: Can not execute SonarQube analysis: Expected one result (or null) to be returned by selectOne(), but found: 2 -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:sonar-maven-plugin:2.2:sonar (default-cli) on project java-utils: Can not execute SonarQube analysis
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:217)
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:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)
Caused by: org.apache.maven.plugin.MojoExecutionException: Can not execute SonarQube analysis
at org.codehaus.mojo.sonar.Bootstraper.executeMojo(Bootstraper.java:109)
at org.codehaus.mojo.sonar.Bootstraper.start(Bootstraper.java:67)
at org.codehaus.mojo.sonar.SonarMojo.execute(SonarMojo.java:109)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
... 19 more
Caused by: org.apache.maven.plugin.MojoExecutionException: Expected one result (or null) to be returned by selectOne(), but found: 2
at org.sonar.maven.ExceptionHandling.handle(ExceptionHandling.java:37)
at org.sonar.maven.SonarMojo.execute(SonarMojo.java:175)
at org.codehaus.mojo.sonar.Bootstraper.executeMojo(Bootstraper.java:104)
... 23 more`enter code here`
Caused by: org.apache.ibatis.exceptions.TooManyResultsException: Expected one result (or null) to be returned by selectOne(), but found: 2
at org.apache.ibatis.session.defaults.DefaultSqlSession.selectOne(DefaultSqlSession.java:66)
at org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:63)
at org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:43)
at com.sun.proxy.$Proxy61.selectByNameAndLanguage(Unknown Source)
at org.sonar.core.qualityprofile.db.QualityProfileDao.selectByNameAndLanguage(QualityProfileDao.java:181)
at org.sonar.core.qualityprofile.db.QualityProfileDao.selectByNameAndLanguage(QualityProfileDao.java:188)
at org.sonar.batch.rule.ModuleQProfiles.loadQProfile(ModuleQProfiles.java:105)
at org.sonar.batch.rule.ModuleQProfiles.(ModuleQProfiles.java:92)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.picocontainer.injectors.AbstractInjector.newInstance(AbstractInjector.java:145)
at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:342)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
at org.picocontainer.injectors.AbstractInjectionFactory$LifecycleAdapter.getComponentInstance(AbstractInjectionFactory.java:56)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631)
at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118)
at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136)
at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78)
at org.picocontainer.injectors.SingleMemberInjector.getMemberArguments(SingleMemberInjector.java:61)
at org.picocontainer.injectors.MethodInjector.getMemberArguments(MethodInjector.java:100)
at org.picocontainer.injectors.MethodInjector$2.run(MethodInjector.java:112)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.MethodInjector.decorateComponentInstance(MethodInjector.java:120)
at org.picocontainer.injectors.CompositeInjector.decorateComponentInstance(CompositeInjector.java:58)
at org.picocontainer.injectors.Reinjector.reinject(Reinjector.java:142)
at org.picocontainer.injectors.ProviderAdapter.getComponentInstance(ProviderAdapter.java:96)
at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631)
at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118)
at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136)
at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78)
at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309)
at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
at org.picocontainer.injectors.AbstractInjectionFactory$LifecycleAdapter.getComponentInstance(AbstractInjectionFactory.java:56)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
at org.picocontainer.DefaultPicoContainer.instantiateComponentAsIsStartable(DefaultPicoContainer.java:1033)
at org.picocontainer.DefaultPicoContainer.addAdapterIfStartable(DefaultPicoContainer.java:1025)
at org.picocontainer.DefaultPicoContainer.startAdapters(DefaultPicoContainer.java:1002)
at org.picocontainer.DefaultPicoContainer.start(DefaultPicoContainer.java:766)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:91)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:199)
at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:194)
at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:187)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
at org.sonar.batch.scan.ScanTask.scan(ScanTask.java:56)
at org.sonar.batch.scan.ScanTask.execute(ScanTask.java:44)
at org.sonar.batch.bootstrap.TaskContainer.doAfterStart(TaskContainer.java:82)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
at org.sonar.batch.bootstrap.BootstrapContainer.executeTask(BootstrapContainer.java:144)
at org.sonar.batch.bootstrap.BootstrapContainer.doAfterStart(BootstrapContainer.java:132)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
at org.sonar.batch.bootstrapper.Batch.startBatch(Batch.java:92)
at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:74)
at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:45)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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:90)
at org.sonar.maven.SonarMojo.execute(SonarMojo.java:173)
... 24 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

You're facing http://jira.codehaus.org/browse/SONAR-5196 that is fixed in the upcoming version (4.3). It means that you have two identical quality profiles (same name but different case) for the same language. Could you delete one and run again an analysis?

Maybe you did not update your SonarQube database. To do this start your SonarQube like
http://<sonarqubeserver>/setup
and follow the instructions there.
This update is sometimes necessary if the upgrade introduces database changes. Nevertheless SonarQube should post a maintenance message if you start it in your browser.

I was the exact same issue. I was 2 quality profiles with the same exact name (after upgrading sonar from 3.5 to 4.2).
I remove the old "sonar way" and keep the new "sonar way" quality profile and it worked.

Thanks for your answers.
I found bunch of "Sonar way" profiles for each language profiles, in actually, I focussed on JAVA profile only.
I renamed all the profiles.
like,
Groovy-Sonar way (from Sonar way for Groovy profiles)
Java-Sonar way (from Sonar way for Java profiles)
JavaScript-Sonar way (from Sonar way for JavaScript profiles)
PHP-Sonar Way (from Sonar way for PHP profiles)
But PHP profiles had "Sonar way" and "Sonar Way". I removed one of them.
and anyway, running Sonar from Jenkins has worked successfully now!
Thank you.

Delete your project that is causing the error in the SonarQube web-interface and then re-scan the project.