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I'm also experiencing this same issue with our Github Enterprise.
Jenkins is also internal, and has access to the github enterprise server.
The plugin is currently configured to check our internal github enterprise every 5 minutes and this same exception is showing in the logs every 5 minutes:
Apr 01, 2014 8:20:52 PM SEVERE org.jenkinsci.plugins.ghprb.GhprbRepository checkState
Error while accessing rate limit API
java.io.FileNotFoundException: http://internal.githubserver.com/api/v3/rate_limit
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1623)
at org.kohsuke.github.Requester.parse(Requester.java:298)
at org.kohsuke.github.Requester._to(Requester.java:175)
at org.kohsuke.github.Requester.to(Requester.java:141)
at org.kohsuke.github.GitHub.getRateLimit(GitHub.java:228)
at org.jenkinsci.plugins.ghprb.GhprbRepository.checkState(GhprbRepository.java:57)
at org.jenkinsci.plugins.ghprb.GhprbRepository.check(GhprbRepository.java:77)
at org.jenkinsci.plugins.ghprb.Ghprb.run(Ghprb.java:72)
at org.jenkinsci.plugins.ghprb.GhprbTrigger.run(GhprbTrigger.java:181)
at hudson.triggers.Trigger.checkTriggers(Trigger.java:258)
at hudson.triggers.Trigger$Cron.doRun(Trigger.java:206)
at hudson.triggers.SafeTimerTask.run(SafeTimerTask.java:54)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:351)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:178)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
System information:
Jenkins Version: 1.556
Jenkins Pull Request Builder Plugin Version: 1.11.2