PMD has been under-reporting violations since Gnag 2.1.0

[stkent]

PMD has been under-reporting violations since Gnag 2.1.0

[stkent]

Here's the PMD report file (build/outputs/gnag/pmd.xml) from the fix-pmd branch as-is:

<?xml version="1.0" encoding="UTF-8"?>
<pmd xmlns="http://pmd.sourceforge.net/report/2.0.0"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://pmd.sourceforge.net/report/2.0.0 http://pmd.sourceforge.net/report_2_0_0.xsd"
    version="6.10.0" timestamp="2019-01-03T21:34:33.940">
<file name="/Users/stkent/dev/personal/libraries/gnag/example-java-kotlin/src/main/java/com/btkelly/gnag/example/JavaFileInJavaSourceSet.java">
<violation beginline="28" endline="28" begincolumn="13" endcolumn="31" rule="CompareObjectsWithEquals" ruleset="Error Prone" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="main" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_errorprone.html#compareobjectswithequals" priority="3">
Use equals() to compare object references.
</violation>
<violation beginline="29" endline="29" begincolumn="13" endcolumn="28" rule="SystemPrintln" ruleset="Best Practices" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="main" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_bestpractices.html#systemprintln" priority="2">
System.out.print is used
</violation>
<violation beginline="33" endline="33" begincolumn="13" endcolumn="28" rule="SystemPrintln" ruleset="Best Practices" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="main" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_bestpractices.html#systemprintln" priority="2">
System.out.print is used
</violation>
<violation beginline="34" endline="34" begincolumn="18" endcolumn="26" rule="AvoidCatchingGenericException" ruleset="Design" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="main" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_design.html#avoidcatchinggenericexception" priority="3">
Avoid catching generic exceptions such as NullPointerException, RuntimeException, Exception in try-catch block
</violation>
<violation beginline="34" endline="36" begincolumn="11" endcolumn="9" rule="EmptyCatchBlock" ruleset="Error Prone" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="main" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_errorprone.html#emptycatchblock" priority="3">
Avoid empty catch blocks
</violation>
<violation beginline="36" endline="38" begincolumn="11" endcolumn="9" rule="EmptyFinallyBlock" ruleset="Error Prone" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="main" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_errorprone.html#emptyfinallyblock" priority="3">
Avoid empty finally blocks
</violation>
<violation beginline="42" endline="44" begincolumn="15" endcolumn="5" rule="UselessOverridingMethod" ruleset="Design" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="finalize" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_design.html#uselessoverridingmethod" priority="3">
Overriding method merely calls super
</violation>
<violation beginline="43" endline="43" begincolumn="9" endcolumn="25" rule="FinalizeOnlyCallsSuperFinalize" ruleset="Error Prone" package="com.btkelly.gnag.example" class="JavaFileInJavaSourceSet" method="finalize" externalInfoUrl="https://pmd.github.io/pmd-6.10.0/pmd_rules_java_errorprone.html#finalizeonlycallssuperfinalize" priority="3">
Finalize should do something besides just calling super.finalize()
</violation>
</file>
<configerror rule="LoosePackageCoupling" msg="No packages or classes specified"/>
</pmd>

Here's the PMD report file (build/outputs/gnag/pmd.xml) from the fix-pmd branch with Checkstyle version bumped to 8.2:

<?xml version="1.0" encoding="UTF-8"?>
<pmd xmlns="http://pmd.sourceforge.net/report/2.0.0"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://pmd.sourceforge.net/report/2.0.0 http://pmd.sourceforge.net/report_2_0_0.xsd"
    version="6.10.0" timestamp="2019-01-03T21:37:24.180">
<error filename="/Users/stkent/dev/personal/libraries/gnag/example-java-kotlin/src/main/java/com/btkelly/gnag/example/JavaFileInJavaSourceSet.java" msg="PMDException: Error while processing /Users/stkent/dev/personal/libraries/gnag/example-java-kotlin/src/main/java/com/btkelly/gnag/example/JavaFileInJavaSourceSet.java">
<![CDATA[net.sourceforge.pmd.PMDException: Error while processing /Users/stkent/dev/personal/libraries/gnag/example-java-kotlin/src/main/java/com/btkelly/gnag/example/JavaFileInJavaSourceSet.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:102)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.MonoThreadProcessor.runAnalysis(MonoThreadProcessor.java:29)
	at net.sourceforge.pmd.processor.AbstractPMDProcessor.processFiles(AbstractPMDProcessor.java:108)
	at net.sourceforge.pmd.PMD.processFiles(PMD.java:329)
	at net.sourceforge.pmd.ant.internal.PMDTaskImpl.doTask(PMDTaskImpl.java:190)
	at net.sourceforge.pmd.ant.internal.PMDTaskImpl.execute(PMDTaskImpl.java:275)
	at net.sourceforge.pmd.ant.PMDTask.execute(PMDTask.java:50)
	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:498)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:352)
	at org.apache.tools.ant.Task$perform.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at com.btkelly.gnag.reporters.PMDViolationDetector.executeReporter(PMDViolationDetector.groovy:65)
	at com.btkelly.gnag.tasks.GnagCheckTask.lambda$executeGnagCheck$0(GnagCheckTask.java:111)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at com.btkelly.gnag.tasks.GnagCheckTask.executeGnagCheck(GnagCheckTask.java:109)
	at com.btkelly.gnag.tasks.GnagCheckTask.taskAction(GnagCheckTask.java:102)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
	at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46)
	at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39)
	at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26)
	at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:794)
	at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:761)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:131)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:317)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:309)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:185)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:97)
	at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:77)
	at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:59)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:59)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:101)
	at org.gradle.api.internal.tasks.execution.FinalizeInputFilePropertiesTaskExecuter.execute(FinalizeInputFilePropertiesTaskExecuter.java:44)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:91)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:62)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:59)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.run(EventFiringTaskExecuter.java:51)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:317)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:309)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:185)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:97)
	at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:46)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$ExecuteTaskAction.execute(DefaultTaskExecutionGraph.java:262)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$ExecuteTaskAction.execute(DefaultTaskExecutionGraph.java:246)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:136)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:130)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.execute(DefaultTaskPlanExecutor.java:201)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.executeWithTask(DefaultTaskPlanExecutor.java:192)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:130)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:74)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph.execute(DefaultTaskExecutionGraph.java:131)
	at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
	at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
	at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
	at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
	at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46)
	at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
	at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
	at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:343)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:317)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:309)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:185)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:97)
	at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
	at org.gradle.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:212)
	at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:140)
	at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:115)
	at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:77)
	at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:74)
	at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
	at org.gradle.internal.work.StopShieldingWorkerLeaseService.withLocks(StopShieldingWorkerLeaseService.java:38)
	at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:96)
	at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:74)
	at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
	at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
	at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
	at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$3.run(RunAsBuildOperationBuildActionRunner.java:47)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:317)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:309)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:185)
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:97)
	at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
	at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:43)
	at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
	at org.gradle.launcher.exec.InProcessBuildActionExecuter$1.transform(InProcessBuildActionExecuter.java:50)
	at org.gradle.launcher.exec.InProcessBuildActionExecuter$1.transform(InProcessBuildActionExecuter.java:46)
	at org.gradle.composite.internal.DefaultRootBuildState.run(DefaultRootBuildState.java:65)
	at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:46)
	at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:32)
	at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
	at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
	at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80)
	at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53)
	at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:62)
	at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:34)
	at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
	at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
	at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
	at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
	at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:59)
	at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:31)
	at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59)
	at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44)
	at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:46)
	at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30)
	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:122)
	at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
	at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
	at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
	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:122)
	at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:55)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
	at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62)
	at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
	at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82)
	at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
	at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
	at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.SecurityException: class "net.sf.saxon.om.Item"'s signer information does not match signer information of other classes in the same package
	at java.lang.ClassLoader.checkCerts(ClassLoader.java:898)
	at java.lang.ClassLoader.preDefineClass(ClassLoader.java:668)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:761)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at net.sourceforge.pmd.lang.rule.XPathRule.initRuleQueryBasedOnVersion(XPathRule.java:145)
	at net.sourceforge.pmd.lang.rule.XPathRule.initXPathRuleQuery(XPathRule.java:128)
	at net.sourceforge.pmd.lang.rule.XPathRule.getRuleChainVisits(XPathRule.java:151)
	at net.sourceforge.pmd.lang.rule.AbstractRule.isRuleChain(AbstractRule.java:310)
	at net.sourceforge.pmd.lang.rule.AbstractDelegateRule.isRuleChain(AbstractDelegateRule.java:311)
	at net.sourceforge.pmd.lang.rule.AbstractDelegateRule.isRuleChain(AbstractDelegateRule.java:311)
	at net.sourceforge.pmd.lang.rule.AbstractRuleChainVisitor.initialize(AbstractRuleChainVisitor.java:158)
	at net.sourceforge.pmd.lang.rule.AbstractRuleChainVisitor.visitAll(AbstractRuleChainVisitor.java:63)
	at net.sourceforge.pmd.RuleChain.apply(RuleChain.java:67)
	at net.sourceforge.pmd.RuleSets.apply(RuleSets.java:140)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:184)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:96)
	... 154 more
]]>
</error>
<configerror rule="LoosePackageCoupling" msg="No packages or classes specified"/>
</pmd>

[stkent]

Snippets from dependency reports on fix-pmd branch (../gradlew dependencies), important lines marked with <---:

Using Checkstyle 8.1:

+--- com.puppycrawl.tools:checkstyle:8.1
|    +--- antlr:antlr:2.7.7
|    +--- org.antlr:antlr4-runtime:4.7
|    +--- commons-beanutils:commons-beanutils:1.9.3
|    |    +--- commons-logging:commons-logging:1.2
|    |    \--- commons-collections:commons-collections:3.2.2
|    +--- commons-cli:commons-cli:1.4
|    \--- com.google.guava:guava:22.0
|         +--- com.google.code.findbugs:jsr305:1.3.9 -> 2.0.1
|         +--- com.google.errorprone:error_prone_annotations:2.0.18
|         +--- com.google.j2objc:j2objc-annotations:1.1
|         \--- org.codehaus.mojo:animal-sniffer-annotations:1.14

...

\--- net.sourceforge.pmd:pmd-java:6.10.0
     +--- net.java.dev.javacc:javacc:5.0
     +--- net.sourceforge.pmd:pmd-core:6.10.0
     |    +--- org.antlr:antlr4-runtime:4.7
     |    +--- com.beust:jcommander:1.72
     |    +--- commons-io:commons-io:2.6
     |    +--- net.java.dev.javacc:javacc:5.0
     |    +--- net.sourceforge.saxon:saxon:9.1.0.8                 <---
     |    +--- org.apache.commons:commons-lang3:3.8.1
     |    +--- org.ow2.asm:asm:6.2.1
     |    \--- com.google.code.gson:gson:2.5
     +--- net.sourceforge.saxon:saxon:9.1.0.8                      <---

Using Checkstyle 8.2:

+--- com.puppycrawl.tools:checkstyle:8.2
|    +--- antlr:antlr:2.7.7
|    +--- org.antlr:antlr4-runtime:4.7
|    +--- commons-beanutils:commons-beanutils:1.9.3
|    |    +--- commons-logging:commons-logging:1.2
|    |    \--- commons-collections:commons-collections:3.2.2
|    +--- commons-cli:commons-cli:1.4
|    +--- com.google.guava:guava:23.0
|    |    +--- com.google.code.findbugs:jsr305:1.3.9 -> 2.0.1
|    |    +--- com.google.errorprone:error_prone_annotations:2.0.18
|    |    +--- com.google.j2objc:j2objc-annotations:1.1
|    |    \--- org.codehaus.mojo:animal-sniffer-annotations:1.14
|    \--- net.sf.saxon:Saxon-HE:9.8.0-4                            <--- new!

...

\--- net.sourceforge.pmd:pmd-java:6.10.0
     +--- net.java.dev.javacc:javacc:5.0
     +--- net.sourceforge.pmd:pmd-core:6.10.0
     |    +--- org.antlr:antlr4-runtime:4.7
     |    +--- com.beust:jcommander:1.72
     |    +--- commons-io:commons-io:2.6
     |    +--- net.java.dev.javacc:javacc:5.0
     |    +--- net.sourceforge.saxon:saxon:9.1.0.8                 <---
     |    +--- org.apache.commons:commons-lang3:3.8.1
     |    +--- org.ow2.asm:asm:6.2.1
     |    \--- com.google.code.gson:gson:2.5
     +--- net.sourceforge.saxon:saxon:9.1.0.8                      <---
     +--- org.ow2.asm:asm:6.2.1
     +--- commons-io:commons-io:2.6
     \--- org.apache.commons:commons-lang3:3.8.1

To be clear: net.sourceforge.saxon:saxon and net.sf.saxon:Saxon-HE both include classes in the same packages.

[stkent]

Ok, this looks promising: pmd/pmd#1294

Using the outdated one, causes problems in projects that use have e.g. both PMD and checkstyle as a dependency (like qulice) because checkstyle uses the newer saxon and there are conflicts between classes used.

qulice is YAGC (yet another Gnag competitor) that has run into the same issue as we have.

The PMD folks have these things to say:

I just checked the qulice code and it's embedding all tools without isolation, so they fail where Maven can succeed when using the checkstyle and pmd plugins on their own.

A later comment offers some suggestions for addressing this problem, though they are Maven-specific. It also sounds like this issue may go away when PMD 7 is released, but that there's no guarantee it won't resurface in the future?

[stkent]

FWIW the PMD folks seem to have been a bit optimistic as to when v7 will release; right now they are ~20% of the way to their milestone (https://github.com/pmd/pmd/milestone/19).

[stkent]

Forcing both PMD and Checkstyle to use the older saxon seems to work:

https://github.com/teamed/qulice/pull/924/files#diff-114c410e043b6604a613c64a6616f3b6

[I have not verified that Checkstyle does not use dynamic checks on the saxon version to enable functionality.]

@btkelly let me know if you are interested in that workaround or if you'd instead prefer to look for a more robust long-term solution.