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Description of problem:
When shutting down from Gnome, gnome fails to clear the "Install Pending Updates" option if updates are installed via another mechanism, such as straight from the command line.

Version-Release number of selected component (if applicable):
gnome-shell-3.14.4-53.el7.x86_64

How reproducible:
100%

Steps to Reproduce:
1. When updates are available, goto shutdown, and see the option
2. Cancel the shutdown.
3. run yum upgrade
4. When finished, goto shutdown. The option is still there.

Actual results:
The option is still there.

Expected results:
The option should be gone.

Additional info:
The option persists, even after restart.

This bug used to exist in Fedora, but it has since been resolved.

I'm not sure if gnome-shell is the correct package to report this against, or if it is some other package like gnome-session.

That sounds like a PackageKit issue.

After evaluating this issue, there are no plans to address it further or fix it in an upcoming release.  Therefore, it is being closed.  If plans change such that this issue will be fixed in an upcoming release, then the bug can be reopened.