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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