I recently ran into some issues with Jenkins timing out if the console log is inactive for too long. I originally had a job with command similar to "make >build.log 2>&1" with a warning publisher tied to that "build.log" file. I changed the job command to simply "make" and modified the job to search for warnings on the console log rather than the old log file. The build itself completes fine, but the final job steps produce an exception.

It seems like this may be because the job has older builds with identical warning category but different warning source, but haven't looked too much into it. A segment of the log containing the error is below:

[WARNINGS] Parsing warnings in console log with parser GNU Make + GNU Compiler (gcc)
ERROR: Publisher hudson.plugins.warnings.WarningsPublisher aborted due to exception
java.lang.NullPointerException
at hudson.plugins.analysis.util.model.AbstractAnnotation.equals(AbstractAnnotation.java:499)
at com.google.common.collect.RegularImmutableSet.contains(RegularImmutableSet.java:54)
at java.util.AbstractSet.removeAll(AbstractSet.java:176)
at hudson.plugins.analysis.core.AnnotationDifferencer.difference(AnnotationDifferencer.java:43)
at hudson.plugins.analysis.core.AnnotationDifferencer.getNewAnnotations(AnnotationDifferencer.java:27)
at hudson.plugins.analysis.core.BuildResult.initialize(BuildResult.java:261)
at hudson.plugins.analysis.core.BuildResult.<init>(BuildResult.java:215)
at hudson.plugins.warnings.WarningsResult.<init>(WarningsResult.java:52)
at hudson.plugins.warnings.WarningsResult.<init>(WarningsResult.java:46)
at hudson.plugins.warnings.WarningsPublisher.annotate(WarningsPublisher.java:406)
at hudson.plugins.warnings.WarningsPublisher.parseConsoleLog(WarningsPublisher.java:365)
at hudson.plugins.warnings.WarningsPublisher.perform(WarningsPublisher.java:276)
at hudson.plugins.analysis.core.HealthAwareRecorder.perform(HealthAwareRecorder.java:289)
at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:19)
...