Hi Warren-
Thanks for the reply. Fink adds /sw/lib to the beginning of the
DYLD_LIBRARY_PATH. Adding the following to the beginning of the
shell script fixed the problem:
DYLD_LIBRARY_PATH=/usr/local/lib
Thanks,
Doug
On Jun 10, 2005, at 2:11 PM, Warren DeLano wrote:
Doug,
I can't be sure, but this looks like a problem with MacOS X binding
PyMOL to
the wrong shared object, quite possibly due to some change in the
resolution
order...your analysis is on track. To fix this, try to figure out
what
entry in PATH, LD_LIBRARY_PATH, (or whatever mechanism MacOS uses
for shared
object resolution) is causing the problem.
You may then be able to simply change the order of the entries in
order to
get things to work correctly.
Alternatively, you could reset the environment variable within your
macpymol
shell script...
Cheers,
Warren
-----Original Message-----
Hi All-
I've been using a shell script called 'macpymol' to start
PyMOL from the command line under OS X (pre-Tiger):
#!/bin/sh
/Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL $*
usage: macpymol file.pdb
I noticed if I use Fink to install an application under OS X
(Tiger) that requires image libraries to be complied and
installed (e.g. /sw/ lib/libJPEG.dylib), PyMOL fails to start
using the above command and gives the following error output
(from the terminal):
File "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/
__init__.py", line 90, in ?
import pymol
File "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/
__init__.py", line 306, in ?
import _cmd
ImportError: Failure linking new module: /Applications/
PyMOLX11Hybrid.app/pymol/modules/pymol/_cmd.so: Symbol not found:
__cg_jpeg_resync_to_restart
Referenced from: /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
ImageIO.framework/
Versions/A/ImageIO
Expected in: /sw/lib/libJPEG.dylib
If I uninstall all Fink installed image libraries (jpeg, png,
etc.), PyMOL starts w/ no problems. If I click directly on
the PyMOLX11Hybrid.app icon, PyMOL starts w/ no problems.
Any idea of how to resolve this so that I can start PyMOL
from the command line? I think it could have something to do
with Fink's /sw/ bin/init.csh adding some /sw info near the
beginning of my $PATH.
Many thanks,
Doug
