[phenixbb] MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and Coot

[Engin Özkan]

Dear Ralf and Ben,

One of our lab members was having this problem, and I am happy to report 
that unsetting the MACOSX_DEPLOYMENT_TARGET in the start_coot shell 
script seems to resolve the problem on my intel Mac. I haven't tested it 
intensively, but a few coot jobs I initiated from the GUI did start, and 
behave as expected.

Thanks,
Engin

On 12/29/10 8:59 AM, Ralf W. Grosse-Kunstleve wrote:
> Hi Ben,
>
>
> Thanks for the great analysis of the problem.
> Could you try editing the file
>
> $PHENIX/phenix/phenix/command_line/start_coot.sh
>
>
> It is a short file. In the middle you'll see a list of "unset"
> statement. Does it solve the original problem if you add
>
> unset MACOSX_DEPLOYMENT_TARGET
>
> to that list?
> If it does I'll add the line in our sources so that it will be in
> all future phenix installers.
>
> Ralf
>
> ----- Original Message ----
>
>> From: Ben Eisenbraun<bene at hkl.hms.harvard.edu>
>> To: phenixbb at phenix-online.org
>> Sent: Wed, December 29, 2010 8:04:36 AM
>> Subject: [phenixbb] MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and Coot
>>
>>
>> Howdy PHENIXians,
>>
>> One of my users reported this error:
>>
>>     File "/programs/i386-mac/coot/coot-latest/lib/python2.7/sysconfig.py", line
>> 300,  in _init_posix
>>      raise IOError(msg)
>> IOError:  $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.4" but "10.5" during
>> configure
>>
>> The person is running on OS X Intel, using a PHENIX nightly and  trying to
>> call Coot.  It looks like the PHENIX nightlies are built  with
>> MACOSX_DEPLOYMENT_TARGET=10.4, and the Coot I built used M_D_T=10.5  and
>> Python is unhappy about this.
>>
>> It's easy to test this:
>>
>>   $  export MACOSX_DEPLOYMENT_TARGET=10.3
>>   $ phenix.python
>> Traceback (most  recent call last):
>>    File
>> "/programs/i386-mac/phenix/dev-606/phenix-dev-606/build/mac-intel-osx/base/Python.framework/Versions/Current/lib/python2.7/site.py",
>>   line 553, in<module>
>> <snip>
>> IOError:  $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.3" but "10.4" during
>> configure
>>
>> Or if you have access to one of our installations:
>>
>>   $  phenix.python
>> import os
>> os.system('coot')
>>
>> Results in the original  error pasted above.  After playing a bit, I came up
>> with a  workaround.  If you just set the M_D_T to 10.5 before starting Coot
>> and  _after_ starting PHENIX, it all seems to work. E.g. I can start Coot
>> using  this script:
>>
>>   $ cat coot.py
>> #!/usr/bin/env phenix.python
>> import  os
>> os.putenv('MACOSX_DEPLOYMENT_TARGET',  '10.5')
>> os.system('coot')
>>
>> And since the 'coot' binary in the PATH is a  wrapper script, I can just set
>> it in the environment there.
>>
>> My  question is: does Python actually need this?  Is my workaround going  to
>> break something?  I'm not enough of a Pythonista to be able to tell  from
>> looking at the sysconfig code if this will be an issue.  There is a  comment
>> in the source:
>>
>>      # On MacOSX we need to check the  setting of the environment variable
>>      # MACOSX_DEPLOYMENT_TARGET:  configure bases some choices on it so
>>      # it needs to be  compatible.
>>
>> But it's not clear to me when it's going to be used.   I'm almost certainly
>> going to implement the workaround, so I'm mostly posting  this for the list
>> archives and to see if anyone has a better  idea.
>>
>> Thanks.
>>
>> -ben
>>
>> --
>> | Ben Eisenbraun
>> | SBGrid  Consortium                           | http://sbgrid.org       |
>> | Harvard  Medical School                      | http://hms.harvard.edu   |
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>>
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-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111