Not sure this is useful, but I also have a machine on which I have updated to 
El Capitan, but have never installed XQuartz or run X11. There is X11 in 
/Applications/Utilities/.

Here is the info I see

timcox$ cd /usr
timcox$ ls X*
X11:
bin     lib     libexec

X11R6:
bin     lib     libexec

timcox$ ls -Flat /usr/X11*
lrwxr-xr-x  1 root  wheel  3 Oct  2 13:03 /usr/X11R6@ -> X11

/usr/X11:
total 0
drwxr-xr-x@  12 root  wheel   408 Oct  2 13:03 ../
drwxr-xr-x  125 root  wheel  4250 Oct  2 13:03 bin/
drwxr-xr-x   88 root  wheel  2992 Sep 17 09:07 lib/
drwxr-xr-x    5 root  wheel   170 Aug 23 03:51 ./
drwxr-xr-x    3 root  wheel   102 Aug 23 03:51 libexec/

timcox$ ls -Flat /usr/X11/libexec/
total 0
drwxr-xr-x  3 root  wheel  102 Aug 23 03:51 ./
drwxr-xr-x  5 root  wheel  170 Aug 23 03:51 ../
-rwxr-xr-x  1 root  wheel  271 Aug 23 03:51 xquartz_postinst.sh*

That script does contain a rm X11 and a run the x11-select.

Regards,

Tim

> On Oct 09, 2015, at 18:27 , Jeremy Sequoia <[email protected]> wrote:
> 
> OSX provides content in /usr/X11 and /usr/X11R6 as part of the OS which 
> operate just to cause /Applications/Utilities/X11.app to launch.  This 
> X11.app basically just directs users to download XQuartz.
> 
> It also contains a post-install script hook that XQuartz calls as part of its 
> post-install.  This hook calls x11-select and causes all the stubs to be 
> uninstalled.
> 
> I'm curious if affected users just don't have the stubs for some reason.
> 
> Sent from my iPhone...
> 
>> On Oct 9, 2015, at 09:13, Tim Cox <[email protected]> wrote:
>> 
>> I too didn't get the link to /usr/X11R6 until I ran the x11-select manually. 
>> I had installed 278c1 in El Capitan and only /usr/X11 was defined. Sorry, I 
>> don't know what 'were the X11 redirection stubs present at install time?' 
>> means exactly.
>> Afterwards,
>> 
>> ls -Flat /usr/X11*
>> lrwxr-xr-x  1 root  wheel  8 Oct  9 13:26 /usr/X11@ -> /opt/X11
>> lrwxr-xr-x  1 root  wheel  8 Oct  9 13:26 /usr/X11R6@ -> /opt/X11
>> 
>> Tim
>> 
>>> On Oct 09, 2015, at 17:40 , Jeremy Sequoia <[email protected]> wrote:
>>> 
>>> It did both for me.  For the affected users, were the X11 redirection stubs 
>>> present at install time?  The call to x11-select is in its postinstall hook.
>>> 
>>> In any event, the call to x11-select will be in Xquartz's postinstall 
>>> script itself whenever I get some cycles to spin and test another update.
>>> 
>>> Sent from my iPhone...
>>> 
>>>>> On Oct 8, 2015, at 23:52, Martin Costabel <[email protected]> wrote:
>>>>> 
>>>>> On 9/10/15 02:56, Jeremy Huddleston Sequoia wrote:
>>>>> /usr/libexec/x11-select /opt/X11
>>>> 
>>>> Thank you. I confirm that this works (if run as root, anyway). It installs 
>>>> both the /usr/X11 and the /usrX11R6 symlinks (somewhat surprisingly, given 
>>>> that /usr/ is supposed to untouchable now).
>>>> I confirm also that installing Xquartz on 10.11 does *not* install the 
>>>> /usr/X11R6 symlink, only /usr/X11. From discussions on the Fink users 
>>>> lists I gather that this is being observed by others as well.
>>>> 
>>>> -- 
>>>> Martin
>> 


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