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I recently replaced the hard drives on my Mid 2010 Mac Pro, and thus had to reinstall OS X Yosemite. (I went with Yosemite instead of El Capitan because, as the computer is destined to become a file server, I wanted native RAID support.) I started the OS X installation around 5:30 PM last night; at 10:30 PM the computer was stuck on the "Setting up..." screen. I know that OS X installs aren't supposed to take five hours. Is the fact that I have the OS X install flash drive still inserted in the Mac Pro causing this? Or is it something else?

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Rebooting without the OS X flash drive inserted fixed the problem.

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