Re: [IMP-users] running error

What platform are you building on? eg linux or mac, what distribution/os version, swig version?

On Jan 20, 2011, at 3:30 AM, Robert Fenwick wrote:

By modifying the config.py file to include a long list of include directories imp fails to build:

Install file: "kernel/include/constants.h" as "build/include/IMP/constants.h"
g++ -o build/src/kernel_wrap.os -c -Wno-deprecated -Woverloaded-virtual -fPIC -DIMP_SWIG_WRAPPER -Ibuild/include -I/home/fenwick/opt/include -I/home/fenwick/opt/include/boost -I/home/fenwick/opt/include/CGAL -I/home/fenwick/opt/include/Python2.5 -I/home/fenwick/opt/include/python2.5 build/src/kernel_wrap.cpp
build/src/kernel_wrap.cpp: In function 'int SWIG_CanCastAsInteger(double*, double, double)':
build/src/kernel_wrap.cpp:3728: error: 'DBL_EPSILON' was not declared in this scope
scons: *** [build/src/kernel_wrap.os] Error 1
scons: building terminated because of errors.

On 20 Jan 2011, at 12:18, Robert Fenwick wrote:

Hi,

I have installed IMP with the minimal requirements that I think that it needs and everything seems to compile without problems. However when I try to import the python modules I get some nasty import errors.

Any help greatly appreciated.

>>> import IMP.core
>>> import IMP.atom
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/atom/__init__.py", line 28, in <module>
   import _IMP_atom
ImportError: /home/fenwick/opt/lib64/python2.5/site-packages/_IMP_atom.so: undefined symbol: _ZN3IMP4atom14CHARMMTopology32CHARMMSegmentTopologyDataWrapperD1Ev
>>> import IMP.saxs
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/saxs/__init__.py", line 163, in <module>
   import IMP.atom
  File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/atom/__init__.py", line 28, in <module>
   import _IMP_atom
ImportError: /home/fenwick/opt/lib64/python2.5/site-packages/_IMP_atom.so: undefined symbol: _ZN3IMP4atom14CHARMMTopology32CHARMMSegmentTopologyDataWrapperD1Ev

Here is the end of teh build process that appears to have worked.

scons: done building targets.

Enabled dependencies: Boost.FileSystem, Boost.ProgramOptions
Disabled dependencies: OpenMM, Bullet, CGAL, ANN, OpenCV, NetCDF, modeller, FFTW3, GSL

Enabled modules: em, kernel, domino, misc, statistics, container, display, saxs, system, core, algebra, restrainer, benchmark, atom, example
Disabled modules: openmm, cgal, bullet, multifit, gsl, modeller, em2d

Enabled applications: foxs, ligand_score, saxs_tools, em_tools

Enabled systems: Groel, example_system

R. Bryn Fenwick
">
Post-doctoral fellow
Chemistry and Molecular Pharmacology Programme
Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
Baldiri Reixac 10, 08028 Barcelona, SPAIN
Tel. (+34) 9340 20460

R. Bryn Fenwick
">
Post-doctoral fellow
Chemistry and Molecular Pharmacology Programme
Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
Baldiri Reixac 10, 08028 Barcelona, SPAIN
Tel. (+34) 9340 20460

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