VMD-L Mailing List

From: Reid Van Lehn (rvanlehn_at_gmail.com)
Date: Fri Jun 04 2010 - 23:11:38 CDT

Hey guys,

Thank you for the help so far! I'm still not sure what caused all of those
errors but I started the compilation process over. I was using the incorrect
system architecture on my previous builds (MACOSX, whereas now I'm using
MACOSXX86_64) and recreated the plugin directory, and configured using the

 MACOSXX86_64 FLTK TK TCL SILENT

options. Now, upon running 'make' in the vmd/src directory it seems to
compile all of the files successfully, but fails with:

Linking vmd_MACOSXX86_64 ...
ln: ./foobar: File exists
ld: library not found for -ltk8.5-x11
collect2: ld returned 1 exit status
make: *** [vmd_MACOSXX86_64] Error 1

where -ltk8.5-x11 is the first library listed in the LIBS line of the
Makefile. I previously installed tcl and tk to the vmd/lib directory using
the unix installation (not macosx one) with the --enable-64bit flag on. I
can't seem to find any libraries that correspond to the one sought for (the
libtk8.5.dylib file is there, however). I figure this is an issue with my
tcl/tk installation but thought you might be able to offer advice since I
haven't had any luck yet. I do have X11 installed, and the -lx11 library was
found successfully (after modifying my LIBDIRS slightly).

Any advice on this problem would be much appreciated!

Thanks,
Reid

On Fri, Jun 4, 2010 at 6:08 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Reid,
> I'm puzzled by the error you are getting. What compiler and
> version are you using? This error seems to indicate that the
> compiler you're using doesn't like forward class declarations,
> but I see nothing wrong there.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 04, 2010 at 12:36:54PM -0400, Reid Van Lehn wrote:
> > Hi everyone,
> >
> > I'm having an issue compiling from source on Mac OS X. I was able to
> > successfully make the plugins directory using the instructions on the
> > website. I next configure a bare-bones installation using:
> >
> > MACOSX OPENGL FLTK TK NETCDF TCL SILENT
> >
> > as my flags. I have the FLTK, Tcl/Tk and NetCDF packages installed in
> > /vmd/lib, mimicking the set ups in the plugins/build.csh file.
> >
> > However, when I run 'gmake' in the /vmd/src directory, make fails with
> a
> > number of errors in MolFilePlugin.c:
> >
> > ***********
> >
> > Compiling MoleculeGraphics.C --> MoleculeGraphics.o ...
> > Compiling MolFilePlugin.c --> MolFilePlugin.o ...
> > In file included from MolFilePlugin.c:31:
> > MolFilePlugin.h:30: error: syntax error before *Molecule*
> > MolFilePlugin.h:30: warning: data definition has no type or storage
> class
> > MolFilePlugin.h:31: error: syntax error before *Timestep*
> > MolFilePlugin.h:31: warning: data definition has no type or storage
> class
> > MolFilePlugin.h:32: error: syntax error before *AtomSel*
> > MolFilePlugin.h:32: warning: data definition has no type or storage
> class
> > MolFilePlugin.h:33: error: syntax error before *Scene*
> > MolFilePlugin.h:33: warning: data definition has no type or storage
> class
> > MolFilePlugin.h:34: error: syntax error before *QMData*
> > MolFilePlugin.h:34: warning: data definition has no type or storage
> class
> > In file included from MolFilePlugin.c:31:
> > MolFilePlugin.h:42: error: syntax error before *MolFilePlugin*
> >
> > plus many more, also in files utilities.h, Matrix4.h, QMData.h, and
> more
> >
> > *************
> >
> > Looking at the errors, it seems like a lot of the C++ keywords aren't
> > being recognized, and the origin of the errors are all tied to the
> > MolFilePlugin.c/.h and Molecule.h files. I've also tried following the
> > directions from
> http://www.debianclusters.org/index.php/NAMD:_Building_vmd
> > with the same results.
> >
> > Does anyone have an idea of what may be wrong? I can send more
> information
> > as needed.
> >
> > Thank you!
> > Reid Van Lehn
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science