Thanks a lot for the cgal workaround Daniel.

Your comment helped me to sort out my second problem too : a version conflict between /usr/local/ stuff and /sw/include stuff. I removed /usr/local/ occurrences in my config.py and all goes well now

I also spotted what seems to be a minor bug at line 22 of imp/src/modules/em2d/include/filenames_manipulation.h where I think 103400 should be replaced by 103600. At least, doing so I was able to compile and link against the fink installed boost version on my computer (v1.35).

--Ben (schwarz)

Le 23 sept. 2010 à 18:43, Daniel Russel a écrit :

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

--- Benjamin SCHWARZ Email : schwarz@igbmc.fr Voice : +33 (0)3 68 85 47 30 FAX : +33 (0)3 68 85 47 18

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