Okay, I'm not sure what happened, but after I went poking around in things,
the only thing not working is startx. All other commands I've tried,
including pymol, are doing what they're supposed to. However, other X11
commands were also not working so I don't think the problem was pymol.
This solves my immediate problem, so I'm good to continue figuring out fink
and fixing it at a slower pace. But if you want to know what startx is
doing, if I start it without XQuartz already running, I get
> font_cache: Scanning user font directories to generate X11 font caches
> font_cache: Updating FC cache
> xauth: file /Users/gtf/.serverauth.81954 does not exist
>
> font_cache: Done
> /opt/X11/bin/xinit: XFree86_VT property unexpectedly has 0 items instead
of 1
and then it hangs.
If I run startx with XQuartz already running, I get
> font_cache: Scanning user font directories to generate X11 font caches
> font_cache: Updating FC cache
> /opt/X11/share/fonts/encodings: error scanning
> /usr/X11R6/lib/X11/fonts/encodings: error scanning
> font_cache: Done
> xauth: file /Users/gtf/.serverauth.82367 does not exist
>
>
> waiting for X server to begin accepting connections .
> ..
> ..
> ..
and it just continues making those two-dot lines.
I can also try to give a more precise description of "went poking around in
things." (I should also note that fink is my first foray back into tools I
used a long time ago, so I may be doing something that in retrospect will
have been really silly.)
On Wed, Jun 11, 2014 at 12:44 AM, Martin Costabel <costa...@wanadoo.fr>
wrote:
> On 11/06/14 08:18, Alexander Hansen wrote:
>
>> On 6/10/14, 8:14 PM, Matthew Arbo wrote:
>>
>>> Hi,
>>> I can't seem to get pymol to find X11. Whenever I try run it, I get the
>>> following:
>>>
>>> Unable to find application named 'X11'
>>> freeglut (pymol): failed to open display ''
>>> PyMOL: abrupt program termination.
>>>
>>> I've done nothing with fink so far except install it and install pymol
>>> (and all dependencies). I'm on OSX 10.9.3, and have XQuartz installed,
>>> and have checked that the virtual packages are there as it says at
>>> http://www.finkproject.org/faq/usage-packages.php?
>>> phpLang=en#apple-x11-wants-xfree86
>>>
>>> Thanks,
>>> Matthew
>>>
>>>
>>>
>> It appears that it is trying to find X11(.app) by name. I'll cc the
>> maintainer.
>>
>> As a workaround, maybe see if making an alias to XQuartz in the Finder
>> and renaming it X11 works?
>>
>
> I suspect it is a missing symlink /usr/X11R6. Starting X11 first, by
> running a command like xdpyinfo, xlsclients or xterm, should make pymol
> work, too, even if there is no app named 'X11'.
>
> --
> Martin
>
>
>
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