epdp-int clang error

epdpint_clang_error

In file included from ../ecell4/epdp/EGFRDSimulator.hpp:44:
../ecell4/epdp/GreensFunction3DRadInf.hpp:22:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real TOLERANCE = 1e-8;
                      ^           ~~~~
../ecell4/epdp/GreensFunction3DRadInf.hpp:26:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real THETA_TOLERANCE = 1e-5;
                      ^                 ~~~~
../ecell4/epdp/GreensFunction3DRadInf.hpp:28:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real MIN_T = 1e-12;
                      ^       ~~~~~
../ecell4/epdp/GreensFunction3DRadInf.hpp:32:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real H = 4.0;
                      ^   ~~~
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
In file included from ../ecell4/epdp/EGFRDSimulator.hpp:45:
../ecell4/epdp/GreensFunction3DAbsSym.hpp:50:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real CUTOFF = 1e-10;
                      ^        ~~~~~
../ecell4/epdp/GreensFunction3DAbsSym.hpp:54:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real CUTOFF_H = 6.0;
                      ^          ~~~
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
In file included from ../ecell4/epdp/EGFRDSimulator.hpp:46:
../ecell4/epdp/GreensFunction3DAbs.hpp:19:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real TOLERANCE = 1e-8;
                      ^           ~~~~
../ecell4/epdp/GreensFunction3DAbs.hpp:23:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real THETA_TOLERANCE = 1e-5;
                      ^                 ~~~~
../ecell4/epdp/GreensFunction3DAbs.hpp:25:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real MIN_T = 1e-18;
                      ^       ~~~~~
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
In file included from ../ecell4/epdp/EGFRDSimulator.hpp:47:
../ecell4/epdp/GreensFunction3D.hpp:23:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real TOLERANCE = 1e-8;
                      ^           ~~~~
../ecell4/epdp/GreensFunction3D.hpp:25:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real H = 7;
                      ^   ~
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:75:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real SAFETY = 1. + 1e-5;
                      ^        ~~~~~~~~~
../ecell4/epdp/EGFRDSimulator.hpp:76:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real SINGLE_SHELL_FACTOR = .1;
                      ^                     ~~
../ecell4/epdp/EGFRDSimulator.hpp:77:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real DEFAULT_DT_FACTOR = 1e-5;
                      ^                   ~~~~
../ecell4/epdp/EGFRDSimulator.hpp:78:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real CUTOFF_FACTOR = 5.6;
                      ^               ~~~
../ecell4/epdp/EGFRDSimulator.hpp:121:1: warning: 'ImmutativeDomainVisitor' defined as a struct template here but previously declared as a class template [-Wmismatched-tags]
struct ImmutativeDomainVisitor
^
../ecell4/epdp/Domain.hpp:10:1: note: did you mean struct here?
class ImmutativeDomainVisitor;
^~~~~
struct
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:143:1: warning: 'MutativeDomainVisitor' defined as a struct template here but previously declared as a class template [-Wmismatched-tags]
struct MutativeDomainVisitor
^
../ecell4/epdp/Domain.hpp:13:1: note: did you mean struct here?
class MutativeDomainVisitor;
^~~~~
struct
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:7:
../ecell4/epdp/World.hpp:107:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real TOLERANCE = 1e-7;
                      ^           ~~~~
../ecell4/epdp/World.hpp:162:34: note: in instantiation of template class 'WorldTraitsBase<CyclicWorldTraits<double>, double>' requested here
struct CyclicWorldTraits: public WorldTraitsBase<CyclicWorldTraits<TD_>, TD_>
                                 ^
../ecell4/epdp/ParticleContainer.hpp:24:22: note: in instantiation of template class 'CyclicWorldTraits<double>' requested here
    typedef typename traits_type::particle_type particle_type;
                     ^
../ecell4/epdp/ParticleContainerBase.hpp:97:14: note: in instantiation of template class 'ParticleContainer<CyclicWorldTraits<double> >' requested here
    : public ParticleContainer<Ttraits_>
             ^
../ecell4/epdp/World.hpp:217:21: note: in instantiation of template class 'ParticleContainerBase<World<CyclicWorldTraits<double> >, CyclicWorldTraits<double> >' requested here
class World: public ParticleContainerBase<World<Ttraits_>, Ttraits_>
                    ^
../ecell4/epdp/egfrd.hpp:17:9: note: in instantiation of template class 'World<CyclicWorldTraits<double> >' requested here
typedef EGFRDWorld::molecule_info_type MoleculeInfo;
        ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
In file included from ../ecell4/epdp/EGFRDSimulator.hpp:38:
../ecell4/epdp/ParticleSimulator.hpp:41:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real MINIMAL_SEPARATION_FACTOR = (1.0 + 1e-7);
                      ^                           ~~~~~~~~~~~~
../ecell4/epdp/EGFRDSimulator.hpp:51:41: note: in instantiation of template class 'ParticleSimulatorTraitsBase<World<CyclicWorldTraits<double> > >' requested here
struct EGFRDSimulatorTraitsBase: public ParticleSimulatorTraitsBase<Tworld_>
                                        ^
../ecell4/epdp/ParticleSimulator.hpp:90:18: note: in instantiation of template class 'EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > >' requested here
        typename Ttraits_::world_type::traits_type::model_type,
                 ^
../ecell4/epdp/EGFRDSimulator.hpp:172:30: note: in instantiation of template class 'ParticleSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >' requested here
class EGFRDSimulator: public ParticleSimulator<Ttraits_>
                             ^
../ecell4/epdp/egfrd.hpp:95:29: note: in instantiation of template class 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >' requested here
    virtual EGFRDSimulator* create_simulator(
                            ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:75:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real SAFETY = 1. + 1e-5;
                      ^        ~~~~~~~~~
../ecell4/epdp/ParticleSimulator.hpp:90:18: note: in instantiation of template class 'EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > >' requested here
        typename Ttraits_::world_type::traits_type::model_type,
                 ^
../ecell4/epdp/EGFRDSimulator.hpp:172:30: note: in instantiation of template class 'ParticleSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >' requested here
class EGFRDSimulator: public ParticleSimulator<Ttraits_>
                             ^
../ecell4/epdp/egfrd.hpp:95:29: note: in instantiation of template class 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >' requested here
    virtual EGFRDSimulator* create_simulator(
                            ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:76:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real SINGLE_SHELL_FACTOR = .1;
                      ^                     ~~
../ecell4/epdp/EGFRDSimulator.hpp:77:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real DEFAULT_DT_FACTOR = 1e-5;
                      ^                   ~~~~
../ecell4/epdp/EGFRDSimulator.hpp:78:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
    static const Real CUTOFF_FACTOR = 5.6;
                      ^               ~~~
In file included from lib/ecell4/epdp.cpp:265:
../ecell4/epdp/egfrd.hpp:102:31: warning: implicit conversion loses integer precision: 'const Integer' (aka 'const long long') to 'int' [-Wshorten-64-to-32]
                world, model, num_retries_, bd_dt_factor_, user_max_shell_size_);
                              ^~~~~~~~~~~~
../ecell4/epdp/egfrd.hpp:107:31: warning: implicit conversion loses integer precision: 'const Integer' (aka 'const long long') to 'int' [-Wshorten-64-to-32]
                world, model, num_retries_, bd_dt_factor_);
                              ^~~~~~~~~~~~
../ecell4/epdp/egfrd.hpp:111:53: warning: implicit conversion loses integer precision: 'const Integer' (aka 'const long long') to 'int' [-Wshorten-64-to-32]
            return new EGFRDSimulator(world, model, num_retries_);
                       ~~~~~~~~~~~~~~               ^~~~~~~~~~~~
In file included from lib/ecell4/epdp.cpp:251:
In file included from ../ecell4/core/CompartmentSpace.hpp:9:
../ecell4/core/CompartmentSpaceHDF5Writer.hpp:149:13: warning: implicit conversion loses integer precision: 'Integer' (aka 'long long') to 'num_molecules_type' (aka 'unsigned int') [-Wshorten-64-to-32]
            space.num_molecules(species_list[i]);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../ecell4/core/CompartmentSpace.hpp:208:9: note: in instantiation of function template specialization 'ecell4::save_compartment_space<ecell4::CompartmentSpaceHDF5Traits<ecell4::CompartmentSpaceVectorImpl> >' requested here
        save_compartment_space<traits_type>(*this, root);
        ^
In file included from lib/ecell4/epdp.cpp:251:
In file included from ../ecell4/core/CompartmentSpace.hpp:9:
../ecell4/core/CompartmentSpaceHDF5Writer.hpp:203:13: warning: implicit conversion loses integer precision: 'hssize_t' (aka 'long long') to 'const unsigned int' [-Wshorten-64-to-32]
            species_dset.getSpace().getSimpleExtentNpoints());
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../ecell4/core/CompartmentSpace.hpp:214:9: note: in instantiation of function template specialization 'ecell4::load_compartment_space<ecell4::CompartmentSpaceHDF5Traits<ecell4::CompartmentSpaceVectorImpl> >' requested here
        load_compartment_space<traits_type>(root, this);
        ^
In file included from lib/ecell4/epdp.cpp:252:
In file included from ../ecell4/core/ParticleSpace.hpp:14:
../ecell4/core/ParticleSpaceHDF5Writer.hpp:92:38: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
    const unsigned int num_particles(particles.size());
                       ~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~
../ecell4/core/ParticleSpace.hpp:378:9: note: in instantiation of function template specialization 'ecell4::save_particle_space<ecell4::ParticleSpaceVectorImpl>' requested here
        save_particle_space(*this, root);
        ^
In file included from lib/ecell4/epdp.cpp:252:
In file included from ../ecell4/core/ParticleSpace.hpp:14:
../ecell4/core/ParticleSpaceHDF5Writer.hpp:114:39: warning: implicit conversion loses integer precision: 'const serial_type' (aka 'const unsigned long long') to 'int' [-Wshorten-64-to-32]
        h5_particle_table[i].serial = particles[i].first.serial();
                                    ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../ecell4/core/ParticleSpaceHDF5Writer.hpp:190:13: warning: implicit conversion loses integer precision: 'hssize_t' (aka 'long long') to 'const unsigned int' [-Wshorten-64-to-32]
            species_dset.getSpace().getSimpleExtentNpoints());
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../ecell4/core/ParticleSpace.hpp:383:9: note: in instantiation of function template specialization 'ecell4::load_particle_space<ecell4::ParticleSpaceVectorImpl>' requested here
        load_particle_space(root, this);
        ^
In file included from lib/ecell4/epdp.cpp:252:
In file included from ../ecell4/core/ParticleSpace.hpp:14:
../ecell4/core/ParticleSpaceHDF5Writer.hpp:199:13: warning: implicit conversion loses integer precision: 'hssize_t' (aka 'long long') to 'const unsigned int' [-Wshorten-64-to-32]
            particle_dset.getSpace().getSimpleExtentNpoints());
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:7:
In file included from ../ecell4/epdp/World.hpp:17:
In file included from ../ecell4/epdp/./ParticleTraits.hpp:5:
In file included from ../ecell4/epdp/Sphere.hpp:5:
In file included from ../ecell4/epdp/Vector3.hpp:20:
../ecell4/epdp/utils/array_traits.hpp:26:22: error: type 'double' cannot be used prior to '::' because it has no members
    typedef typename T_::value_type type;
                     ^
../ecell4/epdp/linear_algebra.hpp:286:43: note: in instantiation of template class 'element_type_of<double>' requested here
inline T_ multiply(T_ const& p1, typename element_type_of<T_>::type const& p2, typename boost::enable_if<is_vector3<T_> >::type* = 0)
                                          ^
../ecell4/epdp/linear_algebra.hpp:301:17: note: while substituting deduced template arguments into function template 'multiply' [with T_ = double]
    retval[0] = multiply(p1[0], p2[0][0])
                ^
../ecell4/epdp/Box.hpp:298:9: note: in instantiation of function template specialization 'multiply<ecell4::Position3, boost::const_multi_array_ref<double, 2, const double *> >' requested here
        multiply(
        ^
../ecell4/epdp/Shape.hpp:91:12: note: in instantiation of function template specialization 'random_position<boost::_bi::bind_t<double, boost::_mfi::mf2<double, ecell4::GSLRandomNumberGenerator, double, double>,
      boost::_bi::list3<boost::_bi::value<ecell4::GSLRandomNumberGenerator>, boost::_bi::value<double>, boost::_bi::value<double> > > >' requested here
    return random_position(shape, const_cast<Trng&>(rng));
           ^
../ecell4/epdp/CuboidalRegion.hpp:28:18: note: in instantiation of function template specialization 'random_position<Box, boost::_bi::bind_t<double, boost::_mfi::mf2<double, ecell4::GSLRandomNumberGenerator, double, double>,
      boost::_bi::list3<boost::_bi::value<ecell4::GSLRandomNumberGenerator>, boost::_bi::value<double>, boost::_bi::value<double> > > >' requested here
        return ::random_position(base_type::shape(),
                 ^
../ecell4/epdp/World.hpp:892:21: note: in instantiation of member function 'CuboidalRegion<CyclicWorldTraits<double> >::random_position' requested here
                new cuboidal_region_type(
                    ^
../ecell4/epdp/World.hpp:285:9: note: in instantiation of member function 'World<CyclicWorldTraits<double> >::add_world_structure' requested here
        add_world_structure();
        ^
../ecell4/epdp/egfrd.hpp:82:24: note: in instantiation of member function 'World<CyclicWorldTraits<double> >::World' requested here
            return new EGFRDWorld(edge_lengths, matrix_sizes_, rng_);
                       ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:7:
../ecell4/epdp/World.hpp:456:23: warning: implicit conversion loses integer precision: 'const Integer' (aka 'const long long') to 'int' [-Wshorten-64-to-32]
        int data[] = {sizes[0], sizes[1], sizes[2]};
                     ~^~~~~~~~
lib/ecell4/epdp.cpp:4068:33: note: in instantiation of member function 'World<CyclicWorldTraits<double> >::save' requested here
  __pyx_v_self->thisptr->get()->save(__pyx_v_filename);
                                ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:7:
../ecell4/epdp/World.hpp:456:33: warning: implicit conversion loses integer precision: 'const Integer' (aka 'const long long') to 'int' [-Wshorten-64-to-32]
        int data[] = {sizes[0], sizes[1], sizes[2]};
                     ~          ^~~~~~~~
../ecell4/epdp/World.hpp:456:43: warning: implicit conversion loses integer precision: 'const Integer' (aka 'const long long') to 'int' [-Wshorten-64-to-32]
        int data[] = {sizes[0], sizes[1], sizes[2]};
                     ~                    ^~~~~~~~
In file included from lib/ecell4/epdp.cpp:252:
In file included from ../ecell4/core/ParticleSpace.hpp:14:
../ecell4/core/ParticleSpaceHDF5Writer.hpp:92:38: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const unsigned int' [-Wshorten-64-to-32]
    const unsigned int num_particles(particles.size());
                       ~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~
../ecell4/epdp/World.hpp:446:17: note: in instantiation of function template specialization 'ecell4::save_particle_space<World<CyclicWorldTraits<double> > >' requested here
        ecell4::save_particle_space(*this, group.get());
                ^
lib/ecell4/epdp.cpp:4068:33: note: in instantiation of member function 'World<CyclicWorldTraits<double> >::save' requested here
  __pyx_v_self->thisptr->get()->save(__pyx_v_filename);
                                ^
In file included from lib/ecell4/epdp.cpp:252:
In file included from ../ecell4/core/ParticleSpace.hpp:14:
../ecell4/core/ParticleSpaceHDF5Writer.hpp:114:39: warning: implicit conversion loses integer precision: 'const serial_type' (aka 'const unsigned long long') to 'int' [-Wshorten-64-to-32]
        h5_particle_table[i].serial = particles[i].first.serial();
                                    ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../ecell4/core/ParticleSpaceHDF5Writer.hpp:190:13: warning: implicit conversion loses integer precision: 'hssize_t' (aka 'long long') to 'const unsigned int' [-Wshorten-64-to-32]
            species_dset.getSpace().getSimpleExtentNpoints());
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../ecell4/epdp/World.hpp:480:17: note: in instantiation of function template specialization 'ecell4::load_particle_space<World<CyclicWorldTraits<double> > >' requested here
        ecell4::load_particle_space(group, this);
                ^
lib/ecell4/epdp.cpp:4131:33: note: in instantiation of member function 'World<CyclicWorldTraits<double> >::load' requested here
  __pyx_v_self->thisptr->get()->load(__pyx_v_filename);
                                ^
In file included from lib/ecell4/epdp.cpp:252:
In file included from ../ecell4/core/ParticleSpace.hpp:14:
../ecell4/core/ParticleSpaceHDF5Writer.hpp:199:13: warning: implicit conversion loses integer precision: 'hssize_t' (aka 'long long') to 'const unsigned int' [-Wshorten-64-to-32]
            particle_dset.getSpace().getSimpleExtentNpoints());
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:7:
In file included from ../ecell4/epdp/World.hpp:17:
In file included from ../ecell4/epdp/./ParticleTraits.hpp:5:
In file included from ../ecell4/epdp/Sphere.hpp:7:
../ecell4/epdp/Shape.hpp:36:34: error: implicit instantiation of undefined member 'shape_position_type<const Sphere>::argument_is_not_a_shape'
    static const std::size_t x = sizeof(argument_is_not_a_shape);
                                 ^
../ecell4/epdp/Shape.hpp:52:17: note: in instantiation of template class 'shape_position_type<const Sphere>' requested here
inline typename shape_position_type<T_>::type& shape_position(T_& shape)
                ^
../ecell4/epdp/Shape.hpp:84:46: note: while substituting deduced template arguments into function template 'shape_position' [with T_ = const Sphere]
    return distance(p1, cyclic_transpose(p2, shape_position(p1), edge_lengths));
                                             ^
../ecell4/epdp/World.hpp:188:16: note: in instantiation of function template specialization 'distance_cyclic<Sphere, ecell4::Position3>' requested here
        return distance_cyclic(p0, p1, edge_lengths);
               ^
../ecell4/epdp/ParticleContainerBase.hpp:178:29: note: in instantiation of function template specialization 'CyclicWorldTraits<double>::distance<Sphere, ecell4::Position3, ecell4::Position3>' requested here
        return traits_type::distance(lhs, rhs, edge_lengths());
                            ^
../ecell4/epdp/EGFRDSimulator.hpp:416:46: note: in instantiation of function template specialization 'ParticleContainerBase<World<CyclicWorldTraits<double> >, CyclicWorldTraits<double> >::distance<Sphere>' requested here
            length_type const distance(world.distance(shape(offset((*i).second, off)), cmp.position()));
                                             ^
../ecell4/epdp/MatrixSpace.hpp:587:25: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                        collector(values_.begin() + *i, pos_off);
                        ^
../ecell4/epdp/EGFRDSimulator.hpp:3097:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::attempt_single_reaction' requested here
                attempt_single_reaction(domain);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3385:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
../ecell4/epdp/Shape.hpp:35:12: note: member is declared here
    struct argument_is_not_a_shape;
           ^
../ecell4/epdp/Shape.hpp:36:34: error: implicit instantiation of undefined member 'shape_position_type<const Cylinder>::argument_is_not_a_shape'
    static const std::size_t x = sizeof(argument_is_not_a_shape);
                                 ^
../ecell4/epdp/Shape.hpp:52:17: note: in instantiation of template class 'shape_position_type<const Cylinder>' requested here
inline typename shape_position_type<T_>::type& shape_position(T_& shape)
                ^
../ecell4/epdp/Shape.hpp:84:46: note: while substituting deduced template arguments into function template 'shape_position' [with T_ = const Cylinder]
    return distance(p1, cyclic_transpose(p2, shape_position(p1), edge_lengths));
                                             ^
../ecell4/epdp/World.hpp:188:16: note: in instantiation of function template specialization 'distance_cyclic<Cylinder, ecell4::Position3>' requested here
        return distance_cyclic(p0, p1, edge_lengths);
               ^
../ecell4/epdp/ParticleContainerBase.hpp:178:29: note: in instantiation of function template specialization 'CyclicWorldTraits<double>::distance<Cylinder, ecell4::Position3, ecell4::Position3>' requested here
        return traits_type::distance(lhs, rhs, edge_lengths());
                            ^
../ecell4/epdp/EGFRDSimulator.hpp:416:46: note: in instantiation of function template specialization 'ParticleContainerBase<World<CyclicWorldTraits<double> >, CyclicWorldTraits<double> >::distance<Cylinder>' requested here
            length_type const distance(world.distance(shape(offset((*i).second, off)), cmp.position()));
                                             ^
../ecell4/epdp/MatrixSpace.hpp:587:25: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                        collector(values_.begin() + *i, pos_off);
                        ^
../ecell4/epdp/EGFRDSimulator.hpp:3097:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::attempt_single_reaction' requested here
                attempt_single_reaction(domain);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3385:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
../ecell4/epdp/Shape.hpp:35:12: note: member is declared here
    struct argument_is_not_a_shape;
           ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:1956:27: warning: unused variable 'particle_radius' [-Wunused-variable]
        length_type const particle_radius(domain.particle().second.radius());
                          ^
../ecell4/epdp/EGFRDSimulator.hpp:2046:17: note: in instantiation of function template specialization 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::burst<Shell<Sphere, DomainID> >' requested here
                burst(*_domain);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:1946:13: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::burst' requested here
            burst(domain, result);
            ^
../ecell4/epdp/EGFRDSimulator.hpp:1159:13: note: in instantiation of function template specialization 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::burst_domains<std::__1::vector<DomainID, std::__1::allocator<DomainID> > >' requested here
            burst_domains(*domains);
            ^
../ecell4/epdp/EGFRDSimulator.hpp:2134:21: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::clear_volume' requested here
                    clear_volume(::shape(reactant.second), domain.id());
                    ^
../ecell4/epdp/EGFRDSimulator.hpp:3097:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::attempt_single_reaction' requested here
                attempt_single_reaction(domain);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3385:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:1956:27: warning: unused variable 'particle_radius' [-Wunused-variable]
        length_type const particle_radius(domain.particle().second.radius());
                          ^
../ecell4/epdp/EGFRDSimulator.hpp:2056:17: note: in instantiation of function template specialization 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::burst<Shell<Cylinder, DomainID> >' requested here
                burst(*_domain);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:1946:13: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::burst' requested here
            burst(domain, result);
            ^
../ecell4/epdp/EGFRDSimulator.hpp:1159:13: note: in instantiation of function template specialization 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::burst_domains<std::__1::vector<DomainID, std::__1::allocator<DomainID> > >' requested here
            burst_domains(*domains);
            ^
../ecell4/epdp/EGFRDSimulator.hpp:2134:21: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::clear_volume' requested here
                    clear_volume(::shape(reactant.second), domain.id());
                    ^
../ecell4/epdp/EGFRDSimulator.hpp:3097:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::attempt_single_reaction' requested here
                attempt_single_reaction(domain);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3385:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
In file included from ../ecell4/epdp/EGFRDSimulator.hpp:41:
../ecell4/epdp/AnalyticalPair.hpp:43:31: warning: unused variable 'sigma' [-Wunused-variable]
            const length_type sigma(R0 + R1);
                              ^
../ecell4/epdp/EGFRDSimulator.hpp:1584:32: note: in instantiation of member function 'AnalyticalPair<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > >, Shell<Cylinder, DomainID> >::AnalyticalPair' requested here
                new_pair = new cylindrical_pair_type(did, p0, p1, new_shell,
                               ^
../ecell4/epdp/EGFRDSimulator.hpp:1563:16: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::create_pair(const particle_id_pair &, const particle_id_pair &, const position_type &, const position_type
      &, length_type)::factory::operator()' requested here
        struct factory: ImmutativeStructureVisitor<typename world_type::traits_type>
               ^
../ecell4/epdp/EGFRDSimulator.hpp:2840:13: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::create_pair' requested here
            create_pair(
            ^
../ecell4/epdp/EGFRDSimulator.hpp:3057:21: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::form_pair' requested here
                    form_pair(domain, *_possible_partner, neighbors));
                    ^
../ecell4/epdp/EGFRDSimulator.hpp:3155:25: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::form_pair_or_multi' requested here
                    if (form_pair_or_multi(domain, bursted))
                        ^
../ecell4/epdp/EGFRDSimulator.hpp:3385:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
In file included from ../ecell4/epdp/EGFRDSimulator.hpp:41:
../ecell4/epdp/AnalyticalPair.hpp:43:31: warning: unused variable 'sigma' [-Wunused-variable]
            const length_type sigma(R0 + R1);
                              ^
../ecell4/epdp/EGFRDSimulator.hpp:1610:32: note: in instantiation of member function 'AnalyticalPair<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > >, Shell<Sphere, DomainID> >::AnalyticalPair' requested here
                new_pair = new spherical_pair_type(did, p0, p1, new_shell,
                               ^
../ecell4/epdp/EGFRDSimulator.hpp:1563:16: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::create_pair(const particle_id_pair &, const particle_id_pair &, const position_type &, const position_type
      &, length_type)::factory::operator()' requested here
        struct factory: ImmutativeStructureVisitor<typename world_type::traits_type>
               ^
../ecell4/epdp/EGFRDSimulator.hpp:2840:13: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::create_pair' requested here
            create_pair(
            ^
../ecell4/epdp/EGFRDSimulator.hpp:3057:21: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::form_pair' requested here
                    form_pair(domain, *_possible_partner, neighbors));
                    ^
../ecell4/epdp/EGFRDSimulator.hpp:3155:25: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::form_pair_or_multi' requested here
                    if (form_pair_or_multi(domain, bursted))
                        ^
../ecell4/epdp/EGFRDSimulator.hpp:3385:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:3296:51: warning: unused variable 'new_species' [-Wunused-variable]
                        molecule_info_type const& new_species(
                                                  ^
../ecell4/epdp/EGFRDSimulator.hpp:3203:17: note: in instantiation of function template specialization 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event<Shell<Sphere, DomainID> >' requested here
                fire_event(*_domain, event.kind());
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3393:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
In file included from lib/ecell4/epdp.cpp:265:
In file included from ../ecell4/epdp/egfrd.hpp:8:
../ecell4/epdp/EGFRDSimulator.hpp:3296:51: warning: unused variable 'new_species' [-Wunused-variable]
                        molecule_info_type const& new_species(
                                                  ^
../ecell4/epdp/EGFRDSimulator.hpp:3211:17: note: in instantiation of function template specialization 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event<Shell<Cylinder, DomainID> >' requested here
                fire_event(*_domain, event.kind());
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3393:17: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
                fire_event(*_event);
                ^
../ecell4/epdp/EGFRDSimulator.hpp:3426:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::fire_event' requested here
        fire_event(*ev.second);
        ^
../ecell4/epdp/EGFRDSimulator.hpp:1085:9: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::_step' requested here
        _step();
        ^
lib/ecell4/epdp.cpp:4669:28: note: in instantiation of member function 'EGFRDSimulator<EGFRDSimulatorTraitsBase<World<CyclicWorldTraits<double> > > >::step' requested here
    __pyx_v_self->thisptr->step();
                           ^
75 warnings and 3 errors generated.
error: command 'cc' failed with exit status 1
+ PYTHONPATH=/Users/knishida/ecell4//lib/python2.7/site-packages:/usr/local/lib/python2.7/dist-packages:/Users/knishida/Library/Python/2.7/lib/python/site-packages/
+ LD_LIBRARY_PATH=/Users/knishida/ecell4//lib
+ python setup.py test
running test
...........WARN: multiple correspondence found [X(a^1)]
WARN: multiple correspondence skipped [X(a^1)]
....WARN: multiple correspondence skipped [A]
.WARN: multiple correspondence found [R(l^1)]
WARN: multiple correspondence skipped [R(l^1)]
WARN: multiple correspondence found [R(_1^1,l=[_1])]
WARN: multiple correspondence skipped [R(_1^1,l=[_1])]
...WARN: multiple correspondence found [_1(a^1)]
WARN: multiple correspondence skipped [_1(a^1)]
WARN: multiple correspondence found [_1(a^1)]
WARN: multiple correspondence skipped [_1(a^1)]
...WARN: multiple correspondence found [_(ps^1)]
WARN: multiple correspondence skipped [_(ps^1)]
.WARN: multiple correspondence found [A(_1=u^1,ps=[_1])]
WARN: multiple correspondence skipped [A(_1=u^1,ps=[_1])]
.............
----------------------------------------------------------------------
Ran 36 tests in 0.113s

OK
+ cd ..