Copying Nikos as I think he may have the answer right on the tip of his tongue.
Bulk of message posted at the bottom.

On Sat, Jun 27, 2009 at 10:32 AM, Mark Knecht<markkne...@gmail.com> wrote:
> On Sat, Jun 27, 2009 at 10:27 AM, Mark Knecht<markkne...@gmail.com> wrote:
>> On Sat, Jun 27, 2009 at 10:25 AM, Mark Knecht<markkne...@gmail.com> wrote:
>>> On Sat, Jun 27, 2009 at 10:18 AM, Alan McKinnon<alan.mckin...@gmail.com> 
>>> wrote:
>>>> On Saturday 27 June 2009 19:10:43 Mark Knecht wrote:
>>>>> On Sat, Jun 27, 2009 at 2:34 AM, Alan McKinnon<alan.mckin...@gmail.com>
>>>> wrote:
>>>>> > On Saturday 27 June 2009 06:24:12 Mark Knecht wrote:
>>>>> >> On Fri, Jun 26, 2009 at 12:30 PM, Alan 
>>>>> >> McKinnon<alan.mckin...@gmail.com>
>>>>> >
>>>>> > wrote:
>>>>> >> > On Friday 26 June 2009 21:05:01 Mark Knecht wrote:
>>>>> >> >> So the weirdness continues. mesa built but then xorg-server failed
>>>>> >> >> with the same failure:
>>>>> >> >>
>>>>> >> >>
>>>>> >> >>  * >>> SetUID: [chmod go-r] /usr/bin/Xorg ...
>>>>> >> >>                        [ ok ]
>>>>> >> >>
>>>>> >> >> Switching to xorg-x11 OpenGL interface...ln: creating symbolic link
>>>>> >> >> `./libglx.so': File exists
>>>>> >> >> !!! Error: Failed to create /lib/libglx.so
>>>>> >> >
>>>>> >> > Looks like you have a file collision between xorg-server and mesa,
>>>>> >> > which is odd as those packages get a lot of testing.
>>>>> >> >
>>>>> >> > Anything on bugs.gentoo.org?
>>>>> >>
>>>>> >> Unfortunately it seem that there are bug reports on this and more
>>>>> >> unfortunately they have apparently been going on nearly a year now.
>>>>> >> It's not a Gentoo thing specifically as there are Ubuntu, Debian and
>>>>> >> other distros with reports in their forums.
>>>>> >>
>>>>> >> There was a possible by hand fix for it but I'll need to look at that
>>>>> >> over the weekend to see if it makes sense on this machine.
>>>>> >>
>>>>> >> Bummer. I hate banging my head up against a wall made of problems no
>>>>> >> one seems to be fixing.
>>>>> >>
>>>>> >> http://bugs.gentoo.org/247685
>>>>> >
>>>>> > The fix seems (in principle at least) to be brain-dead easy:
>>>>> >
>>>>> > - all ebuilds that merge opengl files should put them in distinct
>>>>> > locations by name to avoid collisions
>>>>> > - the contents of /usr/lib64/opengl/xorg-x11/extensions/ should be
>>>>> > symlinks with a sane default put there by xorg-server and modified by
>>>>> > eselect
>>>>> >
>>>>> > Nikos's comments are especially sane in that thread. Perhaps he'll come
>>>>> > along, see this thread and help you out further.
>>>>> >
>>>>> > I suspect that the temporary workaround will be to delete a symlink and
>>>>> > emerge stuff, then remember to always do this on every future re-emerge
>>>>> >
>>>>> > --
>>>>> > alan dot mckinnon at gmail dot com
>>>>>
>>>>> In concept it does seem fairly straight forward, but to some extent
>>>>> I'm not clear why my previous attempts didn't work, unless the
>>>>> questionable files remained behind. What I attempted to do was
>>>>> completely remove everything X, but I probably didn't specifically
>>>>> remove the stuff in /usr/lib/opengl/xorg-x11/extensions. I was
>>>>> expecting the emerge to do that.
>>>>
>>>> According to the bug report you mentioned earlier, the ebuild is 
>>>> attempting to
>>>> perform eselect too late in the process, which fails, and the ebuild
>>>> immediately exits.
>>>>
>>>> So it's not surprising that dodgy files are left behind which you must 
>>>> remove
>>>> manually.
>>>>
>>>> --
>>>> alan dot mckinnon at gmail dot com
>>>>
>>>>
>>> So I'm little confused by a couple of the postings in that report. I
>>> did emerge -C glproto/eselect/mesa/xorg-server and then made sure
>>> there was nothing left in those directories at all. Should I emerge
>>> eselect, manually do a select, and then emerge the rest of the files?
>>>
>>> Or emerge eselect and maybe mesa, do the eselect, then xorg-server?
>>>
>>> mesa is currently building. glproto created
>>> /usr/lib/opengl/xorg-x11/include, but the other two directories are
>>> there yet.
>>>
>>> Cheers,
>>> Mark
>>>
>>
>> With mesa building in screen I tried the eselect step. It completes
>> normally but the extensions directory isn't there yet so there's
>> nothing to check.
>>
>> [detached]
>> myth12 ~ # eselect opengl list
>> Available OpenGL implementations:
>>  [1]   xorg-x11 *
>> myth12 ~ # eselect opengl set 1
>> Switching to xorg-x11 OpenGL interface... done
>> myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/
>> total 12
>> drwxr-xr-x 3 root root 4096 Jun 27 10:20 .
>> drwxr-xr-x 4 root root 4096 Jun 27 10:20 ..
>> drwxr-xr-x 2 root root 4096 Jun 27 10:20 include
>> myth12 ~ #
>>
>
> Ok, with mesa finished building there are now two more directories
> with some header files added in include and some links and files in
> lib:
>
> myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/
> total 20
> drwxr-xr-x 5 root root 4096 Jun 27 10:28 .
> drwxr-xr-x 4 root root 4096 Jun 27 10:20 ..
> drwxr-xr-x 2 root root 4096 Jun 27 10:28 extensions
> drwxr-xr-x 2 root root 4096 Jun 27 10:28 include
> drwxr-xr-x 2 root root 4096 Jun 27 10:28 lib
> myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/extensions/
> total 8
> drwxr-xr-x 2 root root 4096 Jun 27 10:28 .
> drwxr-xr-x 5 root root 4096 Jun 27 10:28 ..
> myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/include/
> total 716
> drwxr-xr-x 2 root root   4096 Jun 27 10:28 .
> drwxr-xr-x 5 root root   4096 Jun 27 10:28 ..
> -rw-r--r-- 1 root root  90752 Jun 27 10:28 gl.h
> -rw-r--r-- 1 root root 461180 Jun 27 10:28 glext.h
> -rw-r--r-- 1 root root  17155 Jun 27 10:28 glx.h
> -rw-r--r-- 1 root root  34142 Jun 27 10:28 glxext.h
> -rw-r--r-- 1 root root   2453 Jun 27 10:20 glxmd.h
> -rw-r--r-- 1 root root  77887 Jun 27 10:20 glxproto.h
> -rw-r--r-- 1 root root  10613 Jun 27 10:20 glxtokens.h
> myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/lib
> total 456
> drwxr-xr-x 2 root root   4096 Jun 27 10:28 .
> drwxr-xr-x 5 root root   4096 Jun 27 10:28 ..
> -rw-r--r-- 1 root root    743 Jun 27 10:28 libGL.la
> lrwxrwxrwx 1 root root     12 Jun 27 10:28 libGL.so -> libGL.so.1.2
> lrwxrwxrwx 1 root root     12 Jun 27 10:28 libGL.so.1 -> libGL.so.1.2
> -rwxr-xr-x 1 root root 448056 Jun 27 10:28 libGL.so.1.2
> myth12 ~ #
>
> Still no problem doing a set in eselect. OK so far... (I think)
>
> myth12 ~ # eselect opengl list
> Available OpenGL implementations:
>  [1]   xorg-x11 *
> myth12 ~ # eselect opengl set 1
> Switching to xorg-x11 OpenGL interface... done
> myth12 ~ #
>
> Now I'll emerge xorg-server.
>
> Cheers,
> Mark
>

OK - so now I'm not so sure what the correct next step is. The
xorg-server emerge completed cleanly but the contents of the
extensions directory are a single file, not a link and now eselect
opengl set 1 fails:

myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/
total 20
drwxr-xr-x 5 root root 4096 Jun 27 10:28 .
drwxr-xr-x 4 root root 4096 Jun 27 10:20 ..
drwxr-xr-x 2 root root 4096 Jun 27 10:57 extensions
drwxr-xr-x 2 root root 4096 Jun 27 10:28 include
drwxr-xr-x 2 root root 4096 Jun 27 10:28 lib
myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/extensions/
total 340
drwxr-xr-x 2 root root   4096 Jun 27 10:57 .
drwxr-xr-x 5 root root   4096 Jun 27 10:28 ..
-rwxr-xr-x 1 root root 334456 Jun 27 10:57 libglx.so
myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/include/
total 716
drwxr-xr-x 2 root root   4096 Jun 27 10:28 .
drwxr-xr-x 5 root root   4096 Jun 27 10:28 ..
-rw-r--r-- 1 root root  90752 Jun 27 10:28 gl.h
-rw-r--r-- 1 root root 461180 Jun 27 10:28 glext.h
-rw-r--r-- 1 root root  17155 Jun 27 10:28 glx.h
-rw-r--r-- 1 root root  34142 Jun 27 10:28 glxext.h
-rw-r--r-- 1 root root   2453 Jun 27 10:20 glxmd.h
-rw-r--r-- 1 root root  77887 Jun 27 10:20 glxproto.h
-rw-r--r-- 1 root root  10613 Jun 27 10:20 glxtokens.h
myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/lib/
total 456
drwxr-xr-x 2 root root   4096 Jun 27 10:28 .
drwxr-xr-x 5 root root   4096 Jun 27 10:28 ..
-rw-r--r-- 1 root root    743 Jun 27 10:28 libGL.la
lrwxrwxrwx 1 root root     12 Jun 27 10:28 libGL.so -> libGL.so.1.2
lrwxrwxrwx 1 root root     12 Jun 27 10:28 libGL.so.1 -> libGL.so.1.2
-rwxr-xr-x 1 root root 448056 Jun 27 10:28 libGL.so.1.2
myth12 ~ #


myth12 ~ # eselect opengl list
Available OpenGL implementations:
  [1]   xorg-x11
myth12 ~ # eselect opengl set 1
Switching to xorg-x11 OpenGL interface...ln: creating symbolic link
`./libglx.so': File exists
!!! Error: Failed to create lib/libglx.so
Killed
myth12 ~ #



myth12 ~ # slocate libglx.so
/usr/lib/opengl/xorg-x11/extensions/libglx.so
/usr/lib/xorg/modules/extensions/libglx.so
myth12 ~ # ls -al /usr/lib/opengl/xorg-x11/extensions/libglx.so
-rwxr-xr-x 1 root root 334456 Jun 27 10:57
/usr/lib/opengl/xorg-x11/extensions/libglx.so
myth12 ~ # ls -al /usr/lib/xorg/modules/extensions/libglx.so
lrwxrwxrwx 1 root root 42 Jun 23 16:42
/usr/lib/xorg/modules/extensions/libglx.so ->
//usr//lib/opengl/ati/extensions/libglx.so
myth12 ~ #


The second one is a link that I suppose it broken because it's showing
up in red. However I don't know if it was there after removing
everything and redoing the emerges as I didn't check for it.

Basically, if the 'thing' in extensions is supposed to be a link, then
where is the real libglx.so supposed to go?

Con-fuzed...

- Mark

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