SonarQube Nullpointer on analysis, missing fields or rules parameters - sonarqube

Question

I'm running into a nullpointer exception when running analysis on a java project.
The condition that triggers the analysis failure only happens when I activate certain Rules in the Quality Profile. Particularly, any rule that has a parameter you can override, causes the nullpointer failure. It fails whether or not I provide an override value or if the parameter is left default.
I should note that I can get successful analysis to complete if those particular rules are deactivated in the quality profile. It only seems to be related to certain rules that have parameters.
I can replicate this Nullpointer failure with both the sonar-runner, and the org.sonarqube gradle plugin (v 1.0). So I suspect it is not a problem with the runner or the plugin but some kind of setup issue with the SonarQube server and/or database.
The problem is, I don't know how to go in and fix this issue. The SonarQube database isn't documented (that I'm aware) I suspect that there is something maybe missing in the database but I'm not even sure where they might be.
Any suggestions on where I might look?
Versions:
SonarQube 4.5.2
SonarQube Runner 2.4
Java 1.8.0_40 Oracle Corporation (64-bit)
Mac OS X 10.10.4 x86_64
Here is the stack trace of the error:
INFO: ------------------------------------------------------------------------
INFO: EXECUTION FAILURE
INFO: ------------------------------------------------------------------------
Total time: 1:43.316s
Final Memory: 27M/635M
INFO: ------------------------------------------------------------------------
ERROR: Error during Sonar runner execution
org.sonar.runner.impl.RunnerException: Unable to execute Sonar
at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:91)
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.sonar.runner.Main.executeTask(Main.java:70)
at org.sonar.runner.Main.execute(Main.java:59)
at org.sonar.runner.Main.main(Main.java:53)
Caused by: java.lang.NullPointerException
at org.sonar.api.batch.rule.Checks.getField(Checks.java:180)
at org.sonar.api.batch.rule.Checks.configureFields(Checks.java:167)
at org.sonar.api.batch.rule.Checks.instantiate(Checks.java:152)
at org.sonar.api.batch.rule.Checks.addAnnotatedChecks(Checks.java:127)
at org.sonar.java.SonarComponents.registerTestCheckClasses(SonarComponents.java:128)
at org.sonar.plugins.java.JavaSquidSensor.analyse(JavaSquidSensor.java:82)
at org.sonar.batch.phases.SensorsExecutor.executeSensor(SensorsExecutor.java:79)
at org.sonar.batch.phases.SensorsExecutor.execute(SensorsExecutor.java:70)
at org.sonar.batch.phases.PhaseExecutor.execute(PhaseExecutor.java:119)
at org.sonar.batch.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:194)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:93)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:78)
at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:233)
at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:228)
at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:221)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:93)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:78)
at org.sonar.batch.scan.ScanTask.scan(ScanTask.java:64)
at org.sonar.batch.scan.ScanTask.execute(ScanTask.java:51)
at org.sonar.batch.bootstrap.TaskContainer.doAfterStart(TaskContainer.java:125)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:93)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:78)
at org.sonar.batch.bootstrap.BootstrapContainer.executeTask(BootstrapContainer.java:173)
at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:95)
at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:67)
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)
... 9 more

Answer 1

We solved the problem, and the problem was indeed the Java plugin on the SonarQube server. The solution was to downgrade the Java plugin though. Here are the versions we ended up using:
Checkstyle [checkstyle] 2.2 Analyze Java code with Checkstyle.
Clover [clover] 3.0 Get code coverage with Atlassian Clover.
Cobertura [cobertura] 1.6.3 Get code coverage with Cobertura.
Findbugs [findbugs] 3.1 Analyze Java code with Findbugs 3.0.0.
Java [java] 2.9.1 SonarQube rule engine.
JIRA [jira] 1.2 Connects SonarQube to Atlassian JIRA in various ways.
LDAP [ldap] 1.4 Delegates authentication to LDAP.
PMD [pmd] 2.3 Analyze Java code with PMD.