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NOT Answered. Having looked in /var/log/install.log during two new update requests, I see this on both instances.

SUAppStoreUpdateController: did not start session for 031-10481 (previously installed?)

The session number is different for each package of course. I can verify that both packages are in fact installed, because running them returns the correct version numbers. The packages are Command Line Tools, and Safari.9

Now there is only the question left. Why is the AppStore Update manager listing the updates as being available each day. Even though the packages are already installed.

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I had this and a reboot seemed to solve this - I needed up with AppStore app telling me I had installed command line tools twice – Mark Sep 20 '15 at 16:36
    
It's driving me nuts. It is throwing errors during install, which is probably causing the repeat. But it won't install either with AppStore, softwareupdate, or Pacifist. – Fanney Howarth Sep 21 '15 at 13:55
    
How much spare disk space do you have? – Mark Sep 21 '15 at 14:41
    
226GB on a 1 TB drive – Fanney Howarth Sep 21 '15 at 14:45

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