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I have the same problem with Jenkins 1.600 and 1.601, but with a slightly different error in the "Github Hook Log". I do not have the EnvInject plugin installed.
Using strategy: Default
[poll] Last Built Revision: Revision 11aa79761c883cceac79c26ff8b6f5f777d80965 (refs/remotes/origin/master)
> git --version # timeout=10
> git -c core.askpass=true ls-remote -h g...@github.com:anantn/myrepo.git # timeout=10
ERROR: Failed to record SCM polling
org.eclipse.jgit.errors.InvalidObjectIdException: Invalid id : Process leaked file descriptors. See htt
at org.eclipse.jgit.lib.ObjectId.fromHexString(ObjectId.java:245)
at org.eclipse.jgit.lib.ObjectId.fromString(ObjectId.java:233)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.getHeadRev(CliGitAPIImpl.java:2333)
at hudson.plugins.git.GitSCM.compareRemoteRevisionWithImpl(GitSCM.java:576)
at hudson.plugins.git.GitSCM.compareRemoteRevisionWith(GitSCM.java:526)
at hudson.scm.SCM.compareRemoteRevisionWith(SCM.java:380)
at hudson.scm.SCM.poll(SCM.java:397)
at hudson.model.AbstractProject._poll(AbstractProject.java:1446)
at hudson.model.AbstractProject.poll(AbstractProject.java:1349)
at com.cloudbees.jenkins.GitHubPushTrigger$1.runPolling(GitHubPushTrigger.java:81)
at com.cloudbees.jenkins.GitHubPushTrigger$1.run(GitHubPushTrigger.java:106)
at hudson.util.SequentialExecutionQueue$QueueEntry.run(SequentialExecutionQueue.java:118)
at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)