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Date: Sun, 12 Jan 2014 14:20:34 -0500
From: Ken Jackson <cygwin@jackson.io>
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Subject: Re: How to create hard-dir links that cygwin won't bother?
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On 01/12/2014 12:23 PM, Linda Walsh wrote:
> I have a dual install of cygwin-x86 & xygwin-x86-64 existing
> mostly side by side in root -- but some programs don't play nice.

Are you saying you entered C:\ when setup.exe prompted for a root?

That's addressed in the FAQ where you are "urged not to choose" it.

http://cygwin.com/faq.html#faq.setup.c

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