[phenixbb] MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and Coot

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Wed Dec 29 21:45:07 PST 2010


OK, thanks. The additional unset will be in dev-625 and higher.
Ralf



----- Original Message ----
> From: Engin Özkan <eozkan at stanford.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Sent: Wed, December 29, 2010 7:38:38 PM
> Subject: Re: [phenixbb] MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and 
>Coot
> 
> 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    
>|
> >> _______________________________________________
> >>  phenixbb mailing  list
> >> phenixbb at phenix-online.org
> >>  http://phenix-online.org/mailman/listinfo/phenixbb
> >>
> >  _______________________________________________
> > phenixbb mailing  list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> 
> 
> -- 
> 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
> 
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