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brew doctor giving error on a directory that has been removed

I just installed homebrew and as suggested, I ran the brew doctor command. I am linux newbie and do not know how to fix most of these things. But I would like to ask especially about the following ...
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Bash: Switching from user to root causes issues with prompt

I am on a Mac, running Snow Leopard (if it matters). I am customizing my bash prompt to display things that get pulled from user specific places. For example, I am using Ruby Version Manager to manage ...