I'm trying to install pymol on a MacBook Pro (intel). I've tried three
approaches and hit problems on each of them. After several hours of effort
I thought I'd ask here. Details below. I'd be happy to be able to build in
any way, I guess the problem in Method 1 is probably the easiest to solve.
Thanks for any help...
Regards,
Terry
Method 1.
---------
In the most straightforward effort, I download pymol-0_99rc6-src.tgz and run
python setup.py install
python setup2.py install
./pymol
as instructed. The first two commands run fine. The ./pymol gets me
Fatal Python error: Interpreter not initialized (version mismatch?)
I have 2 versions of python on my machine. I've tried the above using both
the Darwin ports 2.4 version of python (under /opt) and the system 2.3
version. Both give the same error. It's the "import pymol" line in
__init__.py that's causing the fatal error. I also get this error with an
empty PYTHONPATH. The "pymol" file looks fine in both cases: it runs the
correct python with the correct path to the __init__.py file.
As far as I know the error indicates a problem with conflicting Python
frameworks. But I don't know how to fix it. I thought running the system
python (in both invocations of python setup{,2}.py install) would work, but
it does not. It's not an option for me to uninstall python 2.4.
Method 2.
---------
I also downloaded pymol-0_99rc6-bin-macosx-x86-x11.tgz. When I follow the
instructions there, I get
$ ./pymol
dyld: Library not loaded: /usr/X11R6/lib/libGLU.1.dylib
Referenced from:
/Users/terry/s/net/pymol-0_99rc6-bin-macosx-x86-x11/pymol.exe
Reason: image not found
./pymol: line 18: 13684 Trace/BPT trap $PYMOL_PATH/pymol.exe "$@"
and indeed /usr/X11R6/lib/libGLU.1.dylib does not exist. I do have all of
libGLU.1.3.dylib
libGLU.1.dylib -> libGLU.1.3.dylib
libGLU.dylib -> libGLU.1.3.dylib
in /Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/lib but I was unable to get
these to link (either by putting them into /usr/X11R6/lib, by symlinking to
them, or by setting DYLD_LIBRARY_PATH). The loader finds the libraries but
says:
$ ./pymol
dyld: Library not loaded: /usr/X11R6/lib/libGLU.1.dylib
Referenced from:
/Users/terry/s/net/pymol-0_99rc6-bin-macosx-x86-x11/pymol.exe
Reason: no suitable image found. Did find:
/Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/lib/libGLU.1.dylib: can't
map
./pymol: line 18: 13765 Trace/BPT trap $PYMOL_PATH/pymol.exe "$@"
Method 3:
---------
I tried to build completely from source (something I've done before). When
building the ext packages, build.com fails building freeglut:
gcc -g -O2 -o CallbackMaker CallbackMaker-CallbackMaker.o
../../../src/.libs/libglut.a -lm -L/usr/X11R6/lib -lGL -lGLU -lXext -lX11
-lXxf86vm
/usr/bin/ld: warning multiple definitions of symbol _glPointParameteri
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
definition of _glPointParameteri
/usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of _glPointParameteri
/usr/bin/ld: warning multiple definitions of symbol _glPointParameteriv
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
definition of _glPointParameteriv
/usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of _glPointParameteriv
/usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding may
result in errors or different symbols being used
/usr/bin/ld: Undefined symbols:
_glutBitmapHelvetica12
_glutBitmap8By13
_glutBitmap9By15
_glutBitmapHelvetica10
_glutBitmapHelvetica18
_glutBitmapTimesRoman10
_glutBitmapTimesRoman24
_glutStrokeMonoRoman
_glutStrokeRoman
symbol _glPointParameteri used from dynamic library
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
not from earlier dynamic library /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o)
symbol _glPointParameteriv used from dynamic library
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
not from earlier dynamic library /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o)
collect2: ld returned 1 exit status
