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Recently, the user interface of my Mac Mini started to freeze. I can move the mouse, but mouse clicks don't have any effect: I cannot select a different window, right-click on the desktop doesn't open any contextual menu, and the menus on the top bar are not opened.

All I can do is clicking the shut-down button, but I have to press it twice: The first time I press it (and keep it pressed), I hear a "click!" noise I thought produced from the external hard disk; the second time I press it, the computer shuts down.

What could be causing this issue? How can I find the cause?

The first two times it happened, I thought it was Spotlight causing it, but the last time it happened, Spotlight was not indexing the hard disk's content.

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up vote 1 down vote accepted

Could be anything, unfortunately. Is the mini in a well-ventilated area? Could be overheating. The hard drive could be dying. Could just be a corrupted OS install. You'll have to start trying things to eliminate possibilities. (eg: install OS an external drive, boot from that drive, see if it still hangs.)

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kiamlaluno could also try to boot into safe mode by holding down the shift key on boot. – Patience Sep 13 '12 at 22:14

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