Import Chimera Modules
Hello, I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error:
import chimeraInit chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. Any help or advice would be greatly appreciated, Jon Williams
Hi Jon, Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.c... and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries." Tom On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote:
Hello,
I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables.
However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error:
import chimeraInit chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac.
Any help or advice would be greatly appreciated,
Jon Williams
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH variable, and I think this took care of my original problem. However I have encountered a new error: ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib Referenced from: /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib Reason: Incompatible library version: _chimera.dylib requires version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0 This seems like I just need to update my FreeType libraries, but I have not had a chance to try this yet. If you have any other suggestions, those would be appreciated, otherwise I'll send an update when I get a chance. Thanks again, Jon On Mar 15, 2013, at 7:02 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Jon,
Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables
http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.c...
and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries."
Tom
On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote:
Hello,
I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables.
However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error:
import chimeraInit chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac.
Any help or advice would be greatly appreciated,
Jon Williams
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jon, Chimera includes the version of libfreetype.6.dylib it needs. The error must mean you have another older libfreetype.6.dylib on your system that Chimera is getting instead of its own version. The first thing would be to try to locate where the other libfreetype.6.dylib is. I guess Chimera starts on your machine, so somehow it gets the right library. That suggests that you do not have the environment variables that control library loading setup in the same way as Chimera does. I'd suggest you start Chimera, open the IDLE shell window (Tools / General Controls) and print all the environment variables seen by the running Chimera using for example import os for k,v in os.environ.items(): print k,v and see if those differ from what you are trying outside Chimera. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Import Chimera Modules From: Jonathan Williams To: Tom Goddard Date: 3/18/13 8:05 AM
Hi Tom,
Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH variable, and I think this took care of my original problem. However I have encountered a new error:
ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib Referenced from: /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib Reason: Incompatible library version: _chimera.dylib requires version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0
This seems like I just need to update my FreeType libraries, but I have not had a chance to try this yet. If you have any other suggestions, those would be appreciated, otherwise I'll send an update when I get a chance.
Thanks again,
Jon
On Mar 15, 2013, at 7:02 PM, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Jon,
Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables
http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.c...
and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries."
Tom
On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote:
Hello,
I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables.
However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error:
import chimeraInit chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac.
Any help or advice would be greatly appreciated,
Jon Williams
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Good news: I got the chimera modules to import! I think that you were correct about having an older libfreetype.6.dylib that was being used instead of Chimera's version, probably from my Enthought Python Distribution . Overall I believe that my EPD was making things harder for me. So I removed the EPD from my system, set all of the environment variables per the Chimera IDLE, added ~/Resources/lib and ~/Resources/share to PYTHONPATH, and now I'm in business. Thank you for your help and suggestions! Jon On Mar 18, 2013, at 12:49 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Jon,
Chimera includes the version of libfreetype.6.dylib it needs. The error must mean you have another older libfreetype.6.dylib on your system that Chimera is getting instead of its own version. The first thing would be to try to locate where the other libfreetype.6.dylib is. I guess Chimera starts on your machine, so somehow it gets the right library. That suggests that you do not have the environment variables that control library loading setup in the same way as Chimera does. I'd suggest you start Chimera, open the IDLE shell window (Tools / General Controls) and print all the environment variables seen by the running Chimera using for example
import os for k,v in os.environ.items(): print k,v
and see if those differ from what you are trying outside Chimera.
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] Import Chimera Modules From: Jonathan Williams To: Tom Goddard Date: 3/18/13 8:05 AM
Hi Tom,
Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH variable, and I think this took care of my original problem. However I have encountered a new error:
ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib Referenced from: /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib Reason: Incompatible library version: _chimera.dylib requires version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0
This seems like I just need to update my FreeType libraries, but I have not had a chance to try this yet. If you have any other suggestions, those would be appreciated, otherwise I'll send an update when I get a chance.
Thanks again,
Jon
On Mar 15, 2013, at 7:02 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Jon,
Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables
http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.c...
and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries."
Tom
On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote:
Hello,
I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables.
However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error:
> import chimeraInit > chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >
I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac.
Any help or advice would be greatly appreciated,
Jon Williams
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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