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I have been having problems when I go to install the above update. I click 'restart' to allow the computer to update but it never does. The dock and desktop wallpaper remain but the menu bar at the top and all icons on the desktop disappear.

I have the same problem exactly whenever I go to shut down the computer. I click shut down and again the dock and background stay but everything else vanishes. It is as if it has only partially gone through the process. Any help would be greatly appreciated.

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Your problem is in no way related to Security Update 2016-001.

When your Mac want to terminate a system update, it should go through a normal Restart... as the one you see in  > Restart.... And to achieve this restart it must terminate correctly all the processes actually running.

Your actual problem is caused by one process which refuse to exit correctly.

The first and easiest way to diagnose which process is the culprit consists of using the combination to force quit any ill behaving application:

command ⌘option ⌥esc

If my hypothesis is correct you might see a typical application flagged as not responding. This mean that this process became deaf stupid and won't hear the signal sent by the system to tell it to exit. In this case, just kill it with the Force Quit button.

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If you can log out of the account - do that. It will likely show you which program is hung. You can use the force quit option (in the same Apple Menu as log out).

Once you've failed at force quitting apps and logging out, you can force a shut down in terminal (if terminal can open)

sudo shutdown -h now

If that fails, you would hold the power button down and / or pull the power plug.

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I've been having the exact same problem and finally took time to troubleshoot. I restarted in Safe mode (hold down shift after chime). I hold to manually restart (held down power button) because my stalled restart problem wasn't just for to software update--it also got stuck when using the Finder to restart. Once in Safe mode, my Mac automatically picked up the software update process, finished it and restarted on its own. So far, so good now.

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Force your iMac to shut down and restart by holding down the command and control while pressing the power button. When it restarts and the login screen comes up, cklick the restart icon. That worked for me. Had to do it twice since I also had the iTunes update to do.

Edit: I'm sorry, but my solution doesn't solve the actual problem (the iMac not restarting). But it will install the updates that requires a restart. I also discovered that this bug won't let me log out.

  • (Using the same account you used to post the answer allows you to edit your posts without going through the approval queue. You can merge accounts using the Contact link at the bottom of the page.) – grg Sep 21 '16 at 22:54

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