Re: [PyMOL] OSX: fink image libs, pymol and the command line
On Jun 13, 2005, at 16:42, Douglas Kojetin wrote: 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 It doesn't on my installation, which is about a year old and under 10.3. More importantly, it shouldn't. Meddling with DYLD_LIBRARY_PATH other than temporarily for debugging purposes is a good recipe to break a MacOS X system. Your problem with PyMOL is a perfect illustration. Did you consider submitting a bug report to the Fink team? Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
Re: [PyMOL] OSX: fink image libs, pymol and the command line
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
[PyMOL] OSX: fink image libs, pymol and the command line
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
RE: [PyMOL] OSX: fink image libs, pymol and the command line
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 -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin Sent: Friday, June 10, 2005 10:16 AM To: 'pymol' Subject: [PyMOL] OSX: fink image libs, pymol and the command line 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 --- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. Play to win an NEC 61 plasma display: http://www.necitguy.com/?r=20 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
