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:
dyld: Symbol not found: __cg_jpeg_resync_to_restart
ImportError: No module named ply.lex
and
-- 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
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