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 > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users