I'll post this long-winded thing to the users list although it's really for the developers... I'm revisiting the issue of wanting to have access to the numpy pkg (numpy.scipy.org) for a Chimera plugin - a delayed continuation of the problem discussed here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-April/000743.html Here's my situation: I installed chimera-1.2304-osx_x11.dmg. I then built the numpy pkg (from svn) using my system's python (2.4) via 'python setup.py build' and copied the resulting /numpy dir into the chimera /share dir. I then discover/verify 2 things: 1) using my system's python, I can successfully import both Numeric and numpy - Numeric coming from chimera and the numpy that I just built and copied into chimera's /share dir 2) using the python2.4 bundled with chimera, I cannot import both Numeric and numpy. I can always import one (either one), but then get a bizarre error when trying to import the other. --------------------------- More verbosely: I set PYTHONPATH to /Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Num eric:/Applications/Chimera.app/Contents/Resources/share Then check the system python: [macmini:~] heiland% pwd /Users/heiland [macmini:~] heiland% which python /usr/local/bin/python [macmini:~] heiland% ll /usr/local/bin/python lrwxr-xr-x 1 root heiland 68 Jul 27 06:19 /usr/local/bin/python@ -> ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/python [macmini:~] heiland% python Python 2.4.3 (#1, Apr 7 2006, 10:54:33) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import Numeric import numpy from numpy.core.multiarray import typeinfo
Then check the chimera python: /Applications/Chimera.app/Contents/Resources/share [macmini:Contents/Resources/share] heiland% ../bin/python2.4 Python 2.4.3 (#1, Oct 16 2006, 09:43:37) [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import Numeric import numpy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Applications/Chimera.app/Contents/Resources/share/numpy/__init__.py", line 36, in ? import core File "numpy/core/__init__.py", line 8, in ? import numerictypes as nt File "numpy/core/numerictypes.py", line 83, in ? from multiarray import typeinfo, ndarray, array, empty, dtype ImportError: cannot import name typeinfo
----------------------------- OK, it then dawns on me that probably what I really should be doing is building numpy using chimera's python. So, after downloading the chimera (1.2318) OSX headers (http://www.cgl.ucsf.edu/chimera/sourcecode.html ), putting the /include in the /Resources dir, and doing: /Applications/Chimera.app/Contents/Resources/bin/python2.4 setup.py build It all builds fine, but then I have the same bizarre error when trying to import both Numeric and numpy as before. Crap. So I then use 'ldd' to see the dependencies in the different python executables: ldd /Applications/Chimera.app/Contents/Resources/bin/python2.4 /Applications/Chimera.app/Contents/Resources/bin/python2.4: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) [macmini:~] heiland% ldd /Library/Frameworks/Python.framework/Versions/2.4/bin/python /Library/Frameworks/Python.framework/Versions/2.4/bin/python: /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.3) Note the different versions on the libSystem.B.dylib. Some more poking... [macmini:~] heiland% locate libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3) [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) [macmini:~] heiland% ldd /usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.2) ----------------------------- One thing worth noting is the different gcc builds (my system python used a later build, 5250, cf 5247 for chimera's python). I also installed the latest xcode (2.4.1) before doing all this. If you've stayed with me to the end, I congratulate you :) Basic question - any ideas? Would it be possible for the Chimera OSX developers to verify they have the latest xcode? And secondly, do you know how one can the chimera python have the dependency on libSystem.B.dylib v.88.1.2 instead of 71.1.3 ? Thanks, -Randy Fwiw, this link http://mail.python.org/pipermail/pythonmac-sig/2006-April/017310.html seems related to this thread also.