Sorry for the late response. I got away from this side of what i do
over the weekend and yesterday.
dyld: loaded: /bin/sh
dyld: loaded: /usr/lib/libncurses.5.4.dylib, cpu-sub-type: 3
dyld: loaded: /usr/lib/libSystem.B.dylib, cpu-sub-type: 3
dyld: loaded: /usr/lib/libgcc_s.1.dylib, cpu-sub-type: 3
dyld: loaded: /usr/lib/system/libmathCommon.A.dylib, cpu-sub-type: 3
dyld: loaded: /sw/bin/python2.4
dyld: loaded: /usr/lib/libSystem.B.dylib, cpu-sub-type: 3
dyld: loaded: /usr/lib/libstdc++.6.dylib, cpu-sub-type: 3
dyld: loaded: /usr/lib/libgcc_s.1.dylib, cpu-sub-type: 3
dyld: loaded: /usr/lib/system/libmathCommon.A.dylib, cpu-sub-type: 3
dyld: loaded: /sw/lib/python2.4/lib-dynload/time.so
dyld: loaded: /sw/lib/python2.4/lib-dynload/collections.so
dyld: loaded: /sw/lib/python2.4/lib-dynload/strop.so
dyld: loaded: /sw/lib/python2.4/lib-dynload/math.so
dyld: loaded: /sw/lib/pymol-py24/modules/pymol/_cmd.so
dyld: loaded: /sw/lib/libfreeglut.3.dylib
dyld: loaded: /usr/X11R6/lib/libGL.1.dylib, cpu-sub-type: 3
dyld: loaded: /usr/X11R6/lib/libGLU.1.dylib, cpu-sub-type: 3
dyld: loaded: /usr/local/lib/libpng.3.dylib, cpu-sub-type: 3
dyld: loaded: /sw/lib/pymol-py24/modules/pymol/_cmd.so
Traceback (most recent call last):
File "/sw/lib/pymol-py24/modules/pymol/__init__.py", line 109, in ?
import pymol
File "/sw/lib/pymol-py24/modules/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: Failure linking new module:
/sw/lib/pymol-py24/modules/pymol/_cmd.so: Library not loaded:
/sw/lib/libpng.3.dylib
Referenced from: /sw/lib/pymol-py24/modules/pymol/_cmd.so
Reason: Incompatible library version: _cmd.so requires version
16.0.0 or later, but libpng.3.dylib provides version 3.0.0
On 3/1/07, David R. Morrison <[EMAIL PROTECTED]> wrote:
> Aaron,
>
> Can you please try the following command and tell us the result?
>
> env DYLD_PRINT_LIBRARIES=1 pymol
>
> Thanks,
> Dave
>
>
> On Mar 1, 2007, at 4:25 AM, Alexander Hansen wrote:
>
> > On 3/1/07, aaron bryden <[EMAIL PROTECTED]> wrote:
> >> That's what i'm not understanding is why the error listed by pymol is
> >> referring to the one in /sw/lib/libpng.3.dylib which otool says is
> >> version 16. I also tried deleting frozen bubble and still had the
> >> problems. Do i need to completely wipe fink again and reinstall, or
> >> is their some other mechanism in OS X that I don't understand? I
> >> should also note that I've had frozen bubble for a long time with
> >> pymol working and it wasn't until I added a new package (I forget
> >> which one, i think coot though) in fink that I initially had this
> >> problem (though I still do after a fresh install of fink).
> >>
> >> thanks for your help,
> >>
> >
> > Pymol is saying that it _wants_ the version 16 libpng.3.dylib, but is
> > _finding_ the other one. You get the exact same error if you remove
> > Frozen Bubble?
> >
> > The OS X linker for dynamic libraries can be tricky, and pymol has a
> > fairly fragile build process. With Frozen Bubble out of the way, make
> > sure that you only have one libpng.3.dylib hanging around, and try a
> > rebuild.
> >
> >> Aaron
> >> On 2/28/07, David R. Morrison <[EMAIL PROTECTED]> wrote:
> >> >
> >> > On Feb 28, 2007, at 10:23 AM, aaron bryden wrote:
> >> >
> >> > > oops meant to send this to fink-beginners also
> >> > >
> >> > > ---------- Forwarded message ----------
> >> > > From: aaron bryden <[EMAIL PROTECTED]>
> >> > > Date: Feb 27, 2007 2:59 PM
> >> > > Subject: Re: [Fink-beginners] pymol, libpng problems
> >> > > To: "Daniel E. Macks" <[EMAIL PROTECTED]>
> >> > >
> >> > >
> >> > > Thanks for your help.
> >> > >
> >> > >> I just compiled pymol-py24-0.99-4 and don't see any of my
> >> initial
> >> > >> flag
> >> > >> suspicions. So here are some pieces of info that could help us
> >> > >> nail it
> >> > >> down:
> >> > >>
> >> > >> What specific version of which pymol package are you using?
> >> What OS X
> >> > >> version, what CPU type? Which x11 are you using (Apple's X11,
> >> Fink's
> >> > >> xfree86, or Fink's x.org)?
> >> > > pymol-py24 .99-1002
> >> > > OS X version: 10.4.8
> >> > > cpu type: 2GHz Intel Core Duo
> >> > > Apple's X11 version = X11 1.1.3 - XFree86 4.4.0
> >> > > I should add that I am using unstable because pymol is not
> >> > > available for intel
> >> > >>
> >> > >> Is this package being compiled on your machine or is it
> >> downloaded
> >> > >> precompiled? If it's being compiled locally, could you tell
> >> us the
> >> > >> command that created that _cmd.so file (it's the one that
> >> contains
> >> > >> "-o
> >> > >> modules/pymol/_cmd.so", about 6/7 of the way through the build
> >> > >> output).
> >> > > The package is being compiled on my machine. The output of the
> >> command
> >> > > to build _cmd.so is
> >> > >
> >> > > cc -bundle -bundle_loader /sw/bin/python2.4 -flat_namespace -
> >> undefined
> >> > > suppress -o modules/pymol/_cmd.so */*.o ov/src/*.o -no-cpp-
> >> precomp
> >> > > -Wmissing-prototypes -Wno-long-double -O3 -funroll-loops
> >> > > -fomit-frame-pointer -ffast-math -I/sw/include
> >> > > -I/sw/include/python2.4 -I/sw/include/python2.4/Numeric
> >> > > -I/usr/X11R6/include -D_HAVE_LIBPNG -D_PYMOL_MODULE -
> >> D_PYMOL_NUMPY
> >> > > -D_PYMOL_FINK -L/sw/lib -L/usr/X11R6/lib -lglut -lGL -lGLU
> >> -lpng
> >> > > -lz -lm -lX11 -lXext
> >> > >>
> >> > >> Also, the output of these commands:
> >> > >>
> >> > >> otool -L /sw/lib/pymol-py24/modules/pymol/_cmd.
> >> > > otool -L /sw/lib/pymol-py24/modules/pymol/_cmd.so
> >> > > /sw/lib/pymol-py24/modules/pymol/_cmd.so:
> >> > > /sw/lib/libfreeglut.3.dylib (compatibility version
> >> 12.0.0,
> >> > > current version 12.0.0)
> >> > > /usr/X11R6/lib/libGL.1.dylib (compatibility version
> >> 1.2.0,
> >> > > current version 1.2.0)
> >> > > /usr/X11R6/lib/libGLU.1.dylib (compatibility version
> >> 1.3.0,
> >> > > current version 1.3.0)
> >> > > /sw/lib/libpng.3.dylib (compatibility version 16.0.0,
> >> current
> >> > > version 16.0.0)
> >> > > /usr/lib/libz.1.dylib (compatibility version 1.0.0,
> >> current
> >> > > version 1.2.3)
> >> > > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
> >> > > current version 88.3.4)
> >> > > /usr/X11R6/lib/libX11.6.dylib (compatibility version
> >> 6.2.0,
> >> > > current version 6.2.0)
> >> > > /usr/X11R6/lib/libXext.6.dylib (compatibility version
> >> 6.4.0,
> >> > > current version 6.4.0)
> >> > > /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0,
> >> > > current version 1.0.0)
> >> > >
> >> > >
> >> > >> otool -L /sw/lib/libpng.3.dylib
> >> > > otool -L /sw/lib/libpng.3.dylib
> >> > > /sw/lib/libpng.3.dylib:
> >> > > /sw/lib/libpng.3.dylib (compatibility version 16.0.0,
> >> current
> >> > > version 16.0.0)
> >> > > /usr/lib/libz.1.dylib (compatibility version 1.0.0,
> >> current
> >> > > version 1.2.3)
> >> > > /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 88.3.4)
> >> > >> locate libpng.3.dylib
> >> > > locate libpng.3.dylib
> >> > > /Applications/Frozen-Bubble.app/Contents/Frameworks/libpng.
> >> 3.dylib
> >> > > /sw/lib/libpng.3.dylib
> >> >
> >> > OK, so I've just verfied that Frozen-Bubble-1.0.0e does indeed
> >> > install libpng.3.dylib as a framework, and running otool on this
> >> gives
> >> >
> >> > otool -L /Volumes/Frozen-Bubble/Frozen-Bubble.app/Contents/
> >> > Frameworks/libpng.3.dylib
> >> > /Volumes/Frozen-Bubble/Frozen-Bubble.app/Contents/Frameworks/
> >> libpng.
> >> > 3.dylib:
> >> > @executable_path/../Frameworks/libpng.3.dylib
> >> (compatibility
> >> > version 3.0.0, current version 3.0.0)
> >> > @executable_path/../Frameworks/libz.1.dylib (compatibility
> >> > version 1.0.0, current version 1.2.2)
> >> > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
> >> > current version 71.1.1)
> >> >
> >> > So it sounds like this may indeed be the offender, but why does
> >> DYLD
> >> > find it?
> >> >
> >> > -- Dave
> >> >
> >> >
> >> >
> >>
> >> ---------------------------------------------------------------------
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> >
> >
> > --
> > Alexander K. Hansen
> > (akh)
> > Fink Documenter (still)
>
>
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