[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
> >>
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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
>
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