The place X11 was located changed starting in OS X 10.10 from /usr/X11 (where it has been, oh, just about forever) to /opt/X11. That’s the biggest change I can remember. But I doubt that is the problem. (Presumably you have a symbolic link from /usr/X11 pointing to /usr/X11.)
Removing /opt/local from your PATH is a good thing to try. To be even more certain, you might want to try (temporarily) renaming /opt/local to /opt/SOMETHING_ELSE, just in case there is something which assumes that /opt/local is worth looking at (e.g. for libraries).
Wayne
> On 1 Apr 2016, at 01:41, Keith Hamilton <[log in to unmask]> wrote:
>
> Hello,
>
> I am no sure how to turn off MacPorts; the only thing I can think of is to remove the /opt/local from my path?
>
> I commented out this line in my ~/.bash_profile: 'export PATH=/opt/local/bin:/opt/local/sbin:$PATH'
> Now:
> bash-3.2$ echo $PATH
> /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
>
> The error still happens. I'm not sure that it's a problem with OSX10.11 specifically. This same error occurred when I upgraded from OSX10.9 to OSX10.10. I was able to roll my machine back to OSX10.9 to finish what I was working on at the time.
>
>
> Thank you again,
>
> Keith Hamilton
> Graduate Student
> Liang Tong Lab
> Columbia University
> New York, NY
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