I had solved the compiling problem with fenics 1.4.0, but the link problem
still exists.
The error logs of link are very similar with the error logs of fenics 1.3.0.
Thank you very much.
The new error logs
Undefined symbols for architecture x86_64:
"dolfin::RectangleMesh::RectangleMesh(double, double, double, double,
unsigned long, unsigned long, std::basic_string<char, std::char_traits<char>,
std::allocator<char> >)", referenced from:
dolfin::UnitSquareMesh::UnitSquareMesh(unsigned long, unsigned long,
std::basic_string<char, std::char_traits<char>, std::allocator<char> >) in
react_diff.o
"dolfin::dolfin_error(std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, ...)", referenced from:
dolfin::GenericLinearOperator::init_layout(dolfin::GenericVector const&,
dolfin::GenericVector const&, dolfin::GenericLinearOperator*) in react_diff.o
dolfin::GenericMatrix::is_symmetric(double) const in react_diff.o
dolfin::GenericMatrix::data() const in react_diff.o
dolfin::GenericVector::data() const in react_diff.o
dolfin::GenericVector::data() in react_diff.o
"dolfin::error(std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, ...)", referenced from:
dolfin::GenericVector::init(dolfin::TensorLayout const&) in react_diff.o
"dolfin::deprecation(std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, ...)", referenced from:
dolfin::GenericVector::resize(int, unsigned long) in react_diff.o
dolfin::GenericVector::resize(int, std::pair<unsigned long, unsigned
long>) in react_diff.o
dolfin::GenericVector::resize(int, std::pair<unsigned long, unsigned
long>, std::vector<int, std::allocator<int> > const&) in react_diff.o
"dolfin::DofMap::DofMap(std::shared_ptr<ufc::dofmap const>, dolfin::Mesh
const&)", referenced from:
ReactionDiffusion::Form_a_FunctionSpace_0::Form_a_FunctionSpace_0(dolfin::Mesh
const&) in react_diff.o
"dolfin::FiniteElement::FiniteElement(std::shared_ptr<ufc::finite_element
const>)", referenced from:
ReactionDiffusion::Form_a_FunctionSpace_0::Form_a_FunctionSpace_0(dolfin::Mesh
const&) in react_diff.o
"dolfin::FunctionSpace::FunctionSpace(std::shared_ptr<dolfin::Mesh const>,
std::shared_ptr<dolfin::FiniteElement const>,
std::shared_ptr<dolfin::GenericDofMap const>)", referenced from:
ReactionDiffusion::Form_a_FunctionSpace_0::Form_a_FunctionSpace_0(dolfin::Mesh
const&) in react_diff.o
"dolfin::DirichletBC::DirichletBC(dolfin::FunctionSpace const&,
dolfin::GenericFunction const&, dolfin::SubDomain const&,
std::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)",
referenced from:
pde::PdeReactionDiff::PdeReactionDiff(unsigned int, unsigned int, double,
double) in react_diff.o
pde::PdeReactionDiff::PdeReactionDiff(unsigned int, unsigned int, double,
double) in react_diff.o
pde::PdeReactionDiff::setBound(double) in react_diff.o
"dolfin::LUSolver::LUSolver(std::shared_ptr<dolfin::GenericLinearOperator
const>, std::basic_string<char, std::char_traits<char>, std::allocator<char>
>)", referenced from:
pde::PdeReactionDiff::resolve() in react_diff.o
"dolfin::Parameters::operator[](std::basic_string<char,
std::char_traits<char>, std::allocator<char> >)", referenced from:
pde::PdeReactionDiff::resolve() in react_diff.o
"dolfin::plot(dolfin::Variable const&, std::basic_string<char,
std::char_traits<char>, std::allocator<char> >, std::basic_string<char,
std::char_traits<char>, std::allocator<char> >)", referenced from:
pde::PdeReactionDiff::plot() const in react_diff.o
"dolfin::Expression::compute_vertex_values(std::vector<double,
std::allocator<double> >&, dolfin::Mesh const&) const", referenced from:
vtable for pde::Source in react_diff.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [CancerSimu.app/Contents/MacOS/CancerSimu] Error 1
17:15:39: The process "/usr/bin/make" exited with code 2.
Error while building/deploying project CancerSimu (kit: Desktop)
When executing step "Make"
From: Yu, Xiaohui
Sent: Wednesday, September 10, 2014 3:16 PM
To: '[email protected]'
Subject: fenics compiling problem on OS X 10.9
Hi all,
I have a project can pass compiling and run very well on ubuntu. I am trying to
port it to OS X 10.9.
But I ran into a compiling problem.
I asked my compiling problem at this thread.
http://fenicsproject.org/qa/5383/undefined-symbols-dolfin-error-during-link-on-os-x-10-9
I got an answer from johannr<http://fenicsproject.org/qa/user/johannr>. He
recommended me to use fenics 1.4.0 to compile it.
I tried to use 1.4.0 to compile my project, but there are a lot of errors like
these below during compiling.
When I used 1.3.0 to compile my project, I didn't run into any compiling error
except link errors.
Can someone help tell me how to resolve this problem?
Thank you very much.
Compiling errors,
/Applications/FEniCS.app/Contents/Resources/include/dolfin/fem/DofMap.h:66:5:
note: no known conversion for argument 1 from
'boost::shared_ptr<ufc::dofmap>' to 'std::shared_ptr<const ufc::dofmap>'
In file included from ../MultiDimCancerSimu/src/pde/react_diff.h:9:0,
from
../MultiDimCancerSimu/src/env/src/../include/reactiondiffwrapper.h:5,
from
../MultiDimCancerSimu/src/env/src/reactiondiffwrapper.cpp:4:
../MultiDimCancerSimu/src/pde/ReactionDiffusion.h: In constructor
'ReactionDiffusion::CoefficientSpace_diff::CoefficientSpace_diff(const
dolfin::Mesh&, const dolfin::SubDomain&)':
../MultiDimCancerSimu/src/pde/ReactionDiffusion.h:2200:180: error: no matching
function for call to
'dolfin::FiniteElement::FiniteElement(boost::shared_ptr<ufc::finite_element>)'
boost::shared_ptr<const dolfin::FiniteElement>(new
dolfin::FiniteElement(boost::shared_ptr<ufc::finite_element>(new
reactiondiffusion_finite_element_0()))),
/Applications/FEniCS.app/Contents/Resources/include/dolfin/fem/FiniteElement.h:35:9:
note: no known conversion for argument 1 from
'boost::shared_ptr<ufc::finite_element>' to 'const dolfin::FiniteElement&'
In file included from ../MultiDimCancerSimu/src/pde/react_diff.h:9:0,
from
../MultiDimCancerSimu/src/env/src/../include/reactiondiffwrapper.h:5,
from
../MultiDimCancerSimu/src/env/src/reactiondiffwrapper.cpp:4:
../MultiDimCancerSimu/src/pde/ReactionDiffusion.h:2412:157: error: no matching
function for call to 'dolfin::DofMap::DofMap(boost::shared_ptr<ufc::dofmap>,
const dolfin::Mesh&)'
boost::shared_ptr<const dolfin::DofMap>(new
dolfin::DofMap(boost::shared_ptr<ufc::dofmap>(new
reactiondiffusion_dofmap_1()), *mesh)))
^
../MultiDimCancerSimu/src/pde/ReactionDiffusion.h: In member function 'virtual
ufc::cell_integral* reactiondiffusion_form_1::create_default_cell_integral()
const':
../MultiDimCancerSimu/src/pde/ReactionDiffusion.h:2128:60: error: invalid
new-expression of abstract class type
'reactiondiffusion_cell_integral_1_otherwise'
return new reactiondiffusion_cell_integral_1_otherwise();
^
Thanks,<http://fenicsproject.org/qa/user/johannr>
Xiaohui
Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News &
World Report as one of America's "Best Hospitals" in 11 specialties and
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