We have had two occurrances where the JIRA application runs extremely slow or non-responsive. The only way to resolve the issue was to click "New filter" on the Issue Search screen (v6.0.6). I logged a case with Atlassian Support and this is what they stated.
Thank you for contacting Atlassian support. Judging by the error message you mentioned, it seems an issue related to a third-party called Search Linked Issues for JIRA plugin.
In this case, I'd suggest you to disable this plugin temporarily and see if the problem persists. If the problem is solved by disabling this plugin, you may consider getting in touch with the plugin vendor to further investigate this issue.
I hope this information has helped. If you need more assistance, feel free to ask.
Does anyone have any suggestions, or has anyone had this issue?
Ah, yes, I've seen this in a couple of Jira installs, but they were a while ago, and the problems went away in version 5.1 of Jira (with appropriately upgraded plugin).
In this case, I'd take Atlassian's advice - turn the plugin off and see if the problem goes away. If it doesn't, go back to Atlassian. If it does, then raise an issue with Craftware as it's their plugin and they would probably want to know. (Also, make sure you're using the latest version of the plugin)
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