On 25 Oct 2013, at 20:39, Gideon Simpson <[email protected]> wrote:
> Hi, I posted to bitbucket about this, but was curious if anyone had a > solution. I had previously installed (successfully) the macports fenics on > an OS X 10.8.5 machine, and was trying it on a new one. I've had less > success. I end up with the following errors: > > First, I get the following errors during configuration: > > -- Try OpenMP C flag = [-fopenmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Failed > > and likewise for anything involving OpenMP, which surprised me. I also see: > You must be using Clang - it doesn’t support OpenMP. > dyld: Symbol not found: __cg_jpeg_resync_to_restart > > ImportError: No module named ply.lex > Trying installing ‘ply' (py27-ply?) through MacPorts. > and > The below message means you have CGAL 4.3, which just came out and has an interface change. You need to update to the latest DOLFIN or disable CGAL. Garth > -- Found unsuitable Qt version "" from NOTFOUND > -- QT not found, or QT/VTK not enabled in DOLFIN. Not building demo_plot-qt > -- Disabling generation of documentation because Sphinx is missing. > > > During the build phase, I get a sequence of errors like: > > [ 29%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/ImplicitDomainMeshGenerator.cpp.o > cd > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/build/dolfin > && /opt/local/lib/openmpi/bin/mpicxx -DBOOST_UBLAS_NDEBUG > -DDOLFIN_VERSION=\"1.2.0+\" -DHAS_CGAL -DHAS_CHOLMOD -DHAS_CPPUNIT -DHAS_HDF5 > -DHAS_MPI -DHAS_PARMETIS -DHAS_PETSC -DHAS_SCOTCH -DHAS_UMFPACK -DHAS_VTK > -DHAS_ZLIB -Ddolfin_EXPORTS -pipe -Os -arch x86_64 -pipe -Os -arch x86_64 > -Wno-deprecated -DNDEBUG -arch x86_64 -fPIC -isystem > /opt/local/include/vtk-5.10 > -I/opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0 > -I/opt/local/include/libxml2 -isystem /opt/local/include -isystem > /opt/local/lib/petsc/include -isystem /opt/local/include/eigen3 -isystem > /opt/local/include/openmpi -o > CMakeFiles/dolfin.dir/generation/ImplicitDomainMeshGenerator.cpp.o -c > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:77:15: > error: no template named 'Mesh_cell_base_3' in namespace 'CGAL'; did you > mean 'Mesh_vertex_base_3'? > typedef CGAL::Mesh_cell_base_3<Geom_traits, Mesh_domain, > ~~~~~~^~~~~~~~~~~~~~~~ > Mesh_vertex_base_3 > /opt/local/include/CGAL/Mesh_vertex_base_3.h:46:7: note: 'Mesh_vertex_base_3' > declared here > class Mesh_vertex_base_3 > ^ > In file included from > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:29: > In file included from > /opt/local/include/CGAL/Mesh_complex_3_in_triangulation_3.h:38: > /opt/local/include/CGAL/Mesh_3/Mesh_complex_3_in_triangulation_3_base.h:61:30: > error: no type named 'Subdomain_index' in > 'CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_cell_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, C > GAL::Epick, CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_vertex_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_ds_vertex_base_3<void> > > >, > CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_cell_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Tria > ngulation_ds_cell_base_3<void> > > > > > > > >' > typedef typename Tr::Cell::Subdomain_index Subdomain_index; > ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ > /opt/local/include/CGAL/Mesh_complex_3_in_triangulation_3.h:48:10: note: in > instantiation of template class > 'CGAL::Mesh_3::Mesh_complex_3_in_triangulation_3_base<CGAL::Regular_triangulation_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_vertex_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_ds_vertex_base_3<void> > > >, > CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_ > traits_3<CGAL::Epick>, > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_cell_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_ds_cell_base_3<void> > > > > > >' requested here > public Mesh_3::Mesh_complex_3_in_triangulation_3_base<Tr> > ^ > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:128:17: > note: in instantiation of template class > 'CGAL::Mesh_complex_3_in_triangulation_3<CGAL::Regular_triangulation_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_vertex_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_ds_vertex_base_3<v > oid> > > >, > CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_cell_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_ds_cell_base_3<void> > > > > >, int, int>' requested here > C3t3 c3t3 = build_cgal_triangulation<C3t3>(surface, criteria); > ^ > In file included from > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:29: > In file included from > /opt/local/include/CGAL/Mesh_complex_3_in_triangulation_3.h:38: > /opt/local/include/CGAL/Mesh_3/Mesh_complex_3_in_triangulation_3_base.h:62:30: > error: no type named 'Surface_patch_index' in > 'CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, > CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const > boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, > CGAL::Triangulation_cell_base_with_info_3<int, > CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, > > CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const > boost::function<double (CGAL::Point_3<CGAL::Epick>) >> , CGAL::Epick, CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, >> CGAL::Triangulation_vertex_base_with_info_3<int, >> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_ds_vertex_base_3<void> > > >, >> CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >, >> CGAL::Triangulation_cell_base_with_info_3<int, >> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL:: > Triangulation_ds_cell_base_3<void> > > > > > > > >' > typedef typename Tr::Cell::Surface_patch_index Surface_patch_index; > ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ > /opt/local/bin/cmake -E cmake_progress_report > /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/build/CMakeFiles > > > -gideon > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
