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So a bit of an annoyance with the Mac App Store: if it isn't running, it doesn't seem to check for updates. 2 apps I use quite a bit, Evernote and Twitter have both had recent updates and it's taken me a few days, or in the case of one Evernote update, a week to find out about the update (and Evernote included a fix I wanted).

Is there a way to have the App Store check for update on a schedule and notify me somehow, ie dock icon badge or a bounce or through the OSX software update?

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The App Store doesn't offer that functionality by default, and you can't configure or script it to check for updates. So...

The closest you're going to get is automatically opening the App Store so you can look at the icon to check for updates. Here's how to make the App Store open automatically at an interval:

Open iCal and add a new event. Call it something like Check App Store for Updates. Double-click it on the calendar and click the Edit button. Set the repeat menu to Every day or Every week.
You can get it to check at some interval in between (say, every 3 days), by using the Custom... option.

Set the alarm menu to Open File. In the newly-showing second menu under alarm, choose Other... and select the App Store in your Applications folder. Set the last menu under alarm to on date.

This way, iCal will automatically open the App Store at the interval you specified under the repeat menu. Its window will pop up to remind you to look at its icon. When you do, you'll see the number of available updates.

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Definitely a good option! –  Darryl Hein May 13 '11 at 1:52
    
+1 - Ha! Nice answer. –  boehj May 14 '11 at 2:40
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The Store already does check for updates automatically. Leave the App Store icon in the Dock to be notified of available updates. (Little red counter.)

I am not sure how often it checks, though. In my experience it happens shortly after session login.

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Ummmm, not in my experience. I don't get a number in the icon until I manually open the App Store. –  Nathan Greenstein May 14 '11 at 2:41
    
Very interesting. First thing I did when it was released was banish it from the Dock. I'll pop it back on the Dock and check this out. Thanks for the info. –  boehj May 14 '11 at 2:41
    
I can confirm that this doesn't happen on Snow Leopard. Is it possible you're using a different version of Mac OS X? –  Nathan Greenstein Jun 4 '11 at 15:33
    
I think this is limited to system updates, not app updates. System Update in prefs panel can be configured to check for updates periodically. Since in MountainLion the app store now encompasses system updates you'll get notified about them and the icon gets a number. –  Alex Apr 16 '13 at 17:41
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