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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
    – mmmmmm
    Sep 20, 2015 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.
    – Harry McGovern
    Sep 21, 2015 at 13:55
  • How much spare disk space do you have?
    – mmmmmm
    Sep 21, 2015 at 14:41
  • 226GB on a 1 TB drive
    – Harry McGovern
    Sep 21, 2015 at 14:45

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