Compiling error (Undefined symbols for architecture x86_64: ld: symbol(s) not found for architecture x86_64) on macos

[Bin LI]

I tried to compile on MAC OS 10.11.4 using clang compiler and cmake 3.5.1, ending up with following error. Any suggestion? Thank you very much!

[ 86%] Linking CXX shared library libmshr.dylib
Undefined symbols for architecture x86_64:
  "boost::detail::get_tss_data(void const*)", referenced from:
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::get() const in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::get() const in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::get() const in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Triangle_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Triangle_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::get() const in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Segment_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Segment_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::get() const in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Interval_nt<false>, CGAL::Gmpq, CGAL::Lazy_exact_nt<CGAL::Gmpq>, CGAL::To_interval<CGAL::Gmpq> > >::get() const in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Line_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Line_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::get() const in CSGCGALDomain3D.cpp.o
      ...
  "boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)", referenced from:
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::reset(CGAL::Lazy<CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > >*) in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::~thread_specific_ptr() in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::reset(CGAL::Lazy<CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > >*) in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Plane_3<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::~thread_specific_ptr() in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::reset(CGAL::Lazy<CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > >*) in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Point_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::~thread_specific_ptr() in CSGCGALDomain3D.cpp.o
      boost::thread_specific_ptr<CGAL::Lazy<CGAL::Triangle_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Triangle_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > > >::reset(CGAL::Lazy<CGAL::Triangle_2<CGAL::Simple_cartesian<CGAL::Interval_nt<false> > >, CGAL::Triangle_2<CGAL::Simple_cartesian<CGAL::Gmpq> >, CGAL::Gmpq, CGAL::Cartesian_converter<CGAL::Simple_cartesian<CGAL::Gmpq>, CGAL::Simple_cartesian<CGAL::Interval_nt<false> >, CGAL::NT_converter<CGAL::Gmpq, CGAL::Interval_nt<false> > > >*) in CSGCGALDomain3D.cpp.o
      ...
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libmshr.1.7.0dev.dylib] Error 1
make[1]: *** [CMakeFiles/mshr.dir/all] Error 2
make: *** [all] Error 2

[Johannes Ring]

This might be fixed now after d20094cd934eb7ff8d2be02067e18ed6612a2324.

[Benjamin Dam Kehlet]

Yes, can you try again with a fresh pull of master. (I don't have a mac available to test on at the moment).

[Corrado Maurini]

This is fixed now (I work with Bin and we filed the issue together). Thanks! FYI there are still few warnings with clang:

[ 80%] Building CXX object CMakeFiles/mshr.dir/src/TetgenMeshGenerator3D.cpp.o
[ 83%] Building CXX object CMakeFiles/mshr.dir/src/VTPFileReader.cpp.o
[ 86%] Linking CXX shared library libmshr.dylib
[ 86%] Built target mshr
[ 88%] Swig source
Scanning dependencies of target mshrable
[ 91%] Building CXX object CMakeFiles/mshrable.dir/app/mshrable.cpp.o
/opt/HPC/fenics-dev-petsc-stable/include/dolfin/geometry/Point.h:334: Warning 321: 'str' conflicts with a built-in name in python
/opt/HPC/fenics-dev-petsc-stable/include/dolfin/geometry/Point.h:334: Warning 321: 'str' conflicts with a built-in name in python
Scanning dependencies of target _mshr
[ 94%] Building CXX object swig/CMakeFiles/_mshr.dir/mshrPYTHON_wrap.cxx.o
/opt/HPC/src/fenics-dev-petsc-stable/mshr/build/swig/mshrPYTHON_wrap.cxx:4184:133: warning: '&&' within '||' [-Wlogical-op-parentheses]
  if (!(PyBool_Check(obj)||PyArray_IsScalar(obj, Bool)||(PyArray_Check(obj)&&PyArray_SIZE(reinterpret_cast<PyArrayObject*>(obj))==1)&&PyArray_TYPE(reinterpret_cast<PyArrayObject*>(obj))==NPY_BOOL))
                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/HPC/src/fenics-dev-petsc-stable/mshr/build/swig/mshrPYTHON_wrap.cxx:4184:133: note: place parentheses around the '&&' expression to silence this warning
  if (!(PyBool_Check(obj)||PyArray_IsScalar(obj, Bool)||(PyArray_Check(obj)&&PyArray_SIZE(reinterpret_cast<PyArrayObject*>(obj))==1)&&PyArray_TYPE(reinterpret_cast<PyArrayObject*>(obj))==NPY_BOOL))
                                                                                                                                    ^
                                                        (                                                                                                                                          )
/opt/HPC/src/fenics-dev-petsc-stable/mshr/build/swig/mshrPYTHON_wrap.cxx:4214:63: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
    const std::unique_ptr<const std::vector<double>> vertices(std::move(self->get_vertices()));
                                                              ^
/opt/HPC/src/fenics-dev-petsc-stable/mshr/build/swig/mshrPYTHON_wrap.cxx:4214:63: note: remove std::move call here
    const std::unique_ptr<const std::vector<double>> vertices(std::move(self->get_vertices()));
                                                              ^~~~~~~~~~                    ~
/opt/HPC/src/fenics-dev-petsc-stable/mshr/build/swig/mshrPYTHON_wrap.cxx:4226:66: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
    const std::unique_ptr<const std::vector<std::size_t>> facets(std::move(self->get_facets()));
                                                                 ^
/opt/HPC/src/fenics-dev-petsc-stable/mshr/build/swig/mshrPYTHON_wrap.cxx:4226:66: note: remove std::move call here
    const std::unique_ptr<const std::vector<std::size_t>> facets(std::move(self->get_facets()));
                                                                 ^~~~~~~~~~                  ~
[ 97%] Linking CXX executable mshrable
[ 97%] Built target mshrable

[Benjamin Dam Kehlet]

Good. Thanks! Yes, I'm aware of the warnings now. The one from the swig generated code (mshrPYTHON_wrap.cxx) is hard to get rid of, I guess, (gcc also warnings about this) but the others should be trivial to fix.