Re: [IMP-users] IMP svn compiling issues Mac OS X 10.6 fink-64

[Daniel Russel <>]

The CGAL problem is a bug in CGAL. I patched it in CGAL, but while doing that, removed my work-around in IMP. I'll put the work around back in IMP.

I'm a bit perplexed about the other error as the -lboost_program_options should provided the needed symbol. I haven't used fink. I'll think on it for a bit. Could you send the configure lines that scons prints out (the first page or so of output of scons). Thanks.

BTW, if you do scons -k, it will continue to build other things after an error.


On Sep 23, 2010, at 9:25 AM, Benjamin SCHWARZ wrote:

> Hi list
> 
> I try a compilation of IMP svn 6742   on   Macbook laptop OS X 10.6
> *  Fink 64 bits installed (in /sw) with packages : 
>    cgal-4  fftw-3  boost1.35.python26  boost1.35.nopython    gsl   and graphviz 
> *  Ann hand installed in /usr/local
> *  Modeller installed as most recent MAC dmg
> 
> And I have several problems :
> 
> 1.) the compilation process fails on cgal polyhedron compilation
> 
> g++ -o modules/cgal/src/internal/polyhedrons.os -c -Os -fno-common -dynamic -I/BenInstalls/imp-install/imp-debug/include -I/opt/local/include -I/sw/include -Wall -Wno-deprecated -Woverloaded-virtual -g -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/BenInstalls/imp/src/build/include -I/usr/local/include -I/sw/include -I/usr/local/ann/ann_1.1.2/include /BenInstalls/imp/src/modules/cgal/src/internal/polyhedrons.cpp
> In file included from /sw/include/CGAL/Nef_3/SNC_items.h:26,
>                 from /sw/include/CGAL/Nef_3/Default_items.h:21,
>                 from /sw/include/CGAL/Nef_polyhedron_3.h:29,
>                 from /BenInstalls/imp/src/modules/cgal/src/internal/polyhedrons.cpp:8:
> /sw/include/CGAL/Nef_3/Halfedge.h: In member function 'typename Refs::Vector_3 CGAL::Halfedge_base<Refs>::vector() const':
> /sw/include/CGAL/Nef_3/Halfedge.h:110: error: 'ORIGIN' is not a member of 'CGAL'
> /usr/include/c++/4.2.1/bits/stl_function.h: In member function 'bool std::less<_Tp>::operator()(const _Tp&, const _Tp&) const 
> 
> [..] CGAL awful template insult [..]
> 
> /BenInstalls/imp/src/modules/cgal/src/internal/polyhedrons.cpp:100:   instantiated from here
> /usr/include/c++/4.2.1/bits/stl_function.h:227: error: no match for 'operator<' in '__x < __y'
> 
> [..] a few lines with replacement propositions for this operator [..]
> 
> Enabled dependencies:  python, ANN, NetCDF, FFTW3, GSL, CGAL, Boost.ProgramOptions
> Disabled/unfound optional dependencies:  Boost.FileSystem, ExampleLib, Bullet
> 
> Enabled modules:  kernel, cgal, algebra, core, container, atom, display, domino, em, example, misc, saxs, helper, statistics, gsl, modeller, restrainer, domino2, benchmark
> Disabled modules: em2d, multifit, bullet
> Errors building:
>  modules/cgal/src/internal/polyhedrons.os
> 
> 
> 2.) I was then able to continue the compilation by disabling the cgal dependency (cgal="no" in the config.py). It then goes on quite a long time then crashes at link time on :
> 
> g++ -o applications/saxs/profile.o -c -Os -fno-common -dynamic -I/BenInstalls/imp-install/imp-debug/include -I/opt/local/include -I/sw/include -Wall -Wno-deprecated -Woverloaded-virtual -g -Ibuild/include -I/BenInstalls/imp/src/build/include -I/usr/local/include -I/sw/include -I/usr/local/ann/ann_1.1.2/include /BenInstalls/imp/src/applications/saxs/profile.cpp
> g++ -o applications/saxs/foxs -g applications/saxs/profile.o applications/saxs/Gnuplot.o -Lbuild/lib -L/BenInstalls/imp/src/build/lib -L/usr/local/lib -L/sw/lib -L/usr/local/ann/ann_1.1.2/lib -L/BenInstalls/imp-install/imp-debug/lib -limp_saxs -limp_atom -limp_container -limp_core -limp_algebra -limp -lANN -lnetcdf_c++ -lboost_program_options
> ld: warning: directory '/BenInstalls/imp/src/build/lib' following -L not found
> ld: warning: directory '/BenInstalls/imp-install/imp-debug/lib' following -L not found
> Undefined symbols:
>  "boost::program_options::options_description::options_description(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int)", referenced from:
>      _main in profile.o
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> scons: *** [applications/saxs/foxs] Error 1
> scons: building terminated because of errors.
> 
> Any hint appreciated.
> 
>     --Ben Schwarz
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