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Compile error for models mixing alpha-numeric parameter names #259

Closed Auerilas closed 8 years ago

Auerilas commented 8 years ago

Summary:

After upgrading to Xcode 8.0, models that include mixed alpha-numeric characters for parameter names (i.e. B0) no longer compile. This issue has been migrated from the stan mailing list.

Reproducible Steps:

This model compiles fine:

import pystan as past
simple_model = """
... data{
...     int N;
...     vector[N] y;
... }
... parameters{
...     real mu;
...     real<lower=0> sd_y;
... }
... model{
...     y ~ normal(mu, sd_y);
... }
... """

compiledMod = pyst.StanModel(model_code = simple_model)
INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_329eb2439cb72421aa0a1fb3fe8fc983 NOW.

This model fails:

simple_model2 = """
... data{
...     int N;
...     vector[N] y;
... }
... parameters{
...     real B0;
...     real<lower=0> sd_y;
... }
... model{
...     y ~ normal(B0, sd_y);
... }
... """

compiledMod = pyst.StanModel(model_code = simple_model2, verbose=True)
INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_44de3e647405f3e3843ab13a390ccfce NOW.
INFO:pystan:OS: darwin, Python: 3.5.2 |Anaconda custom (x86_64)| (default, Jul  2 2016, 17:52:12) 
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)], Cython 0.24.1
Compiling /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.pyx because it changed.
[1/1] Cythonizing /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.pyx
building 'stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257' extension
creating /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var
creating /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var/folders
creating /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var/folders/zl
creating /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn
creating /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T
creating /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/Nate/anaconda/include -arch x86_64 -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c -I/Users/Nate/anaconda/lib/python3.5/site-packages/pystan -I/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src -I/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/lib/stan_math_2.12.0 -I/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/lib/stan_math_2.12.0/lib/eigen_3.2.9 -I/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/lib/stan_math_2.12.0/lib/boost_1.60.0 -I/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/lib/stan_math_2.12.0/lib/cvodes_2.8.2/include -I/Users/Nate/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/Nate/anaconda/include/python3.5m -c /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp -o /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:339:
In file included from /Users/Nate/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/Nate/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/Nate/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:
/Users/Nate/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: 
      "Using deprecated NumPy API, disable it by "          "#defining
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:112:16: error: 
      expected unqualified-id
        double B0(0);
               ^
/usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'
#define B0      0
                ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:113:12: error: 
      expression is not assignable
        B0 = vals_r__[pos__++];
        ~~ ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:115:41: error: 
      non-const lvalue reference to type 'double' cannot bind to a temporary of
      type 'int'
            writer__.scalar_unconstrain(B0);
                                        ^~
/usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'
#define B0      0
                ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/io/writer.hpp:101:34: note: 
      passing argument to parameter 'y' here
      void scalar_unconstrain(T& y) {
                                 ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: 
      expected unqualified-id
        T__ B0;
            ^
/usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'
#define B0      0
                ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: 
      expected unqualified-id
        double B0 = in__.scalar_constrain();
               ^
/usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'
#define B0      0
                ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8412:30: warning: 
      comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and
      'size_type' (aka 'unsigned long') [-Wsign-compare]
    __pyx_t_12 = ((__pyx_t_9 != __pyx_v_fitptr->param_names_oi().size()) != 0);
                   ~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:19293:77: warning: 
      comparison of integers of different signs: 'size_t' (aka 'unsigned long')
      and 'long' [-Wsign-compare]
  ...= __Pyx_PyInt_As_size_t(__pyx_v_item); if (unlikely(__pyx_t_5 == -1L && ...
                                                         ~~~~~~~~~ ^  ~~~
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:542:43: note: 
      expanded from macro 'unlikely'
  #define unlikely(x) __builtin_expect(!!(x), 0)
                                          ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:19875:83: warning: 
      comparison of integers of different signs: 'unsigned int' and 'int'
      [-Wsign-compare]
  ...if (unlikely(__pyx_t_5 == -1 && PyErr_Occurred())) __PYX_ERR(2, 52, __py...
                  ~~~~~~~~~ ^  ~~
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:542:43: note: 
      expanded from macro 'unlikely'
  #define unlikely(x) __builtin_expect(!!(x), 0)
                                          ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:166:16: error: 
      expression is not assignable
            B0 = in__.scalar_constrain(lp__);
            ~~ ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:217:14: note: 
      in instantiation of function template specialization
      'anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce::log_prob<true,
      true, stan::math::var>' requested here
      return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, stream);

             ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:402:31: note: 
      in instantiation of function template specialization
      'anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce::log_prob<true,
      true, stan::math::var>' requested here
        return model.template log_prob<true, true, T>(x, o);
                              ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/lib/stan_math_2.12.0/stan/math/rev/mat/functor/gradient.hpp:51:22: note: 
      in instantiation of function template specialization
      'stan::model::model_functional<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>::operator()<stan::math::var>'
      requested here
        var fx_var = f(x_var);
                     ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:423:21: note: 
      in instantiation of function template specialization
      'stan::math::gradient<stan::model::model_functional<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>
      >' requested here
        stan::math::gradient(model_functional<M>(model, &ss), x, f, grad_f);
                    ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/services/init/initialize_state.hpp:131:24: note: 
      in instantiation of function template specialization
      'stan::model::gradient<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
          stan::model::gradient(model, cont_params, init_log_prob,
                       ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/services/init/initialize_state.hpp:177:16: note: 
      in instantiation of function template specialization
      'stan::services::init::initialize_state_values<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
        return initialize_state_values(cont_params, model, writer);
               ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/services/init/initialize_state.hpp:429:20: note: 
      in instantiation of function template specialization
      'stan::services::init::initialize_state_zero<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
            return initialize_state_zero(cont_params, model, writer);
                   ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:993:36: note: 
      in instantiation of function template specialization
      'stan::services::init::initialize_state<pystan::io::py_var_context_factory,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
        if (!stan::services::init::initialize_state(init,
                                   ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1751:13: note: 
      in instantiation of function template specialization 'pystan::(anonymous
      namespace)::sampler_command<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
      ret = sampler_command(args, model_, holder, names_oi_tidx_,
            ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8451:34: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::call_sampler' requested here
    __pyx_t_14 = __pyx_v_fitptr->call_sampler((*__pyx_v_argsptr), (*__py...
                                 ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:166:16: error: 
      expression is not assignable
            B0 = in__.scalar_constrain(lp__);
            ~~ ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:225:21: note: 
      in instantiation of function template specialization
      'anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce::log_prob<false,
      true, double>' requested here
          .template log_prob<propto,
                    ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:281:7: note: 
      in instantiation of function template specialization
      'stan::model::finite_diff_grad<false, true,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
      finite_diff_grad<false,
      ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1018:24: note: 
      in instantiation of function template specialization
      'stan::model::test_gradients<true, true,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
          stan::model::test_gradients<true,true>(model,cont_vector,disc_vector,
                       ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1751:13: note: 
      in instantiation of function template specialization 'pystan::(anonymous
      namespace)::sampler_command<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
      ret = sampler_command(args, model_, holder, names_oi_tidx_,
            ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8451:34: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::call_sampler' requested here
    __pyx_t_14 = __pyx_v_fitptr->call_sampler((*__pyx_v_argsptr), (*__py...
                                 ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:345:
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:217:14: error: 
      no matching member function for call to 'log_prob'
      return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, stream);

             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/variational/advi.hpp:115:47: note: 
      in instantiation of function template specialization
      'anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce::log_prob<false,
      true, double>' requested here
            double log_prob = model_.template log_prob<false, true>(zeta, &ss);
                                              ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/variational/advi.hpp:203:23: note: 
      in instantiation of member function
      'stan::variational::advi<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::variational::normal_fullrank,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::calc_ELBO' requested here
          elbo_init = calc_ELBO(variational, message_writer);
                      ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/variational/advi.hpp:499:17: note: 
      in instantiation of member function
      'stan::variational::advi<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::variational::normal_fullrank,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::adapt_eta' requested here
          eta = adapt_eta(variational, adapt_iterations, message_writer);
                ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1116:22: note: 
      in instantiation of member function
      'stan::variational::advi<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::variational::normal_fullrank,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::run' requested here
            cmd_advi.run(eta, adapt_engaged, adapt_iterations, tol_rel_o...
                     ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1751:13: note: 
      in instantiation of function template specialization 'pystan::(anonymous
      namespace)::sampler_command<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
      ret = sampler_command(args, model_, holder, names_oi_tidx_,
            ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8451:34: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::call_sampler' requested here
    __pyx_t_14 = __pyx_v_fitptr->call_sampler((*__pyx_v_argsptr), (*__py...
                                 ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:150:9: note: 
      candidate template ignored: substitution failure [with propto__ = false,
      jacobian__ = true, T__ = double]
    T__ log_prob(vector<T__>& params_r__,
        ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:210:8: note: 
      candidate function template not viable: requires at most 2 arguments, but
      3 were provided
    T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
       ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:343:
In file included from /Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:82:
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/variational/advi.hpp:115:47: error: 
      no matching member function for call to 'log_prob'
            double log_prob = model_.template log_prob<false, true>(zeta, &ss);
                              ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/variational/advi.hpp:203:23: note: 
      in instantiation of member function
      'stan::variational::advi<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::variational::normal_meanfield,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::calc_ELBO' requested here
          elbo_init = calc_ELBO(variational, message_writer);
                      ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/variational/advi.hpp:499:17: note: 
      in instantiation of member function
      'stan::variational::advi<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::variational::normal_meanfield,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::adapt_eta' requested here
          eta = adapt_eta(variational, adapt_iterations, message_writer);
                ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1138:24: note: 
      in instantiation of member function
      'stan::variational::advi<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::variational::normal_meanfield,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::run' requested here
              cmd_advi.run(eta, adapt_engaged, adapt_iterations, tol_rel...
                       ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1751:13: note: 
      in instantiation of function template specialization 'pystan::(anonymous
      namespace)::sampler_command<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
      ret = sampler_command(args, model_, holder, names_oi_tidx_,
            ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8451:34: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::call_sampler' requested here
    __pyx_t_14 = __pyx_v_fitptr->call_sampler((*__pyx_v_argsptr), (*__py...
                                 ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:150:9: note: 
      candidate template ignored: could not match 'vector' against 'Matrix'
    T__ log_prob(vector<T__>& params_r__,
        ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:210:8: note: 
      candidate template ignored: substitution failure [with propto = false,
      jacobian = true, T_ = double]
    T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
       ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:166:16: error: 
      expression is not assignable
            B0 = in__.scalar_constrain(lp__);
            ~~ ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:92:28: note: 
      in instantiation of function template specialization
      'anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce::log_prob<true,
      false, stan::math::var>' requested here
          = model.template log_prob<propto, jacobian_adjust_transform>
                           ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/optimization/bfgs.hpp:347:17: note: 
      in instantiation of function template specialization
      'stan::model::log_prob_grad<true, false,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
          f = - log_prob_grad<true, false>(_model, _x, _params_i, _g, _msgs);
                ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/optimization/bfgs.hpp:151:15: note: 
      in instantiation of member function
      'stan::optimization::ModelAdaptor<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>::operator()'
      requested here
        ret = _func(_xk, _fk, _gk);
              ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/optimization/bfgs.hpp:410:19: note: 
      in instantiation of member function
      'stan::optimization::BFGSMinimizer<stan::optimization::ModelAdaptor<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>,
      stan::optimization::LBFGSUpdate<double, -1>, double, -1>::initialize'
      requested here
        BFGSBase::initialize(x);
                  ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/optimization/bfgs.hpp:402:9: note: 
      in instantiation of member function
      'stan::optimization::BFGSLineSearch<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::optimization::LBFGSUpdate<double, -1>, double, -1>::initialize'
      requested here
        initialize(params_r);
        ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1190:21: note: 
      in instantiation of member function
      'stan::optimization::BFGSLineSearch<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      stan::optimization::LBFGSUpdate<double, -1>, double, -1>::BFGSLineSearch'
      requested here
          Optimizer lbfgs(model, cont_vector, disc_vector, &std::cout);
                    ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1751:13: note: 
      in instantiation of function template specialization 'pystan::(anonymous
      namespace)::sampler_command<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
      ret = sampler_command(args, model_, holder, names_oi_tidx_,
            ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8451:34: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::call_sampler' requested here
    __pyx_t_14 = __pyx_v_fitptr->call_sampler((*__pyx_v_argsptr), (*__py...
                                 ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:343:
In file included from /Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:18:
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:92:28: error: 
      no matching member function for call to 'log_prob'
          = model.template log_prob<propto, jacobian_adjust_transform>
            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1303:36: note: 
      in instantiation of function template specialization
      'stan::model::log_prob_grad<true, true,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
          double lp = stan::model::log_prob_grad<true,true>(model, cont_...
                                   ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1751:13: note: 
      in instantiation of function template specialization 'pystan::(anonymous
      namespace)::sampler_command<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >' requested here
      ret = sampler_command(args, model_, holder, names_oi_tidx_,
            ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:8451:34: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::call_sampler' requested here
    __pyx_t_14 = __pyx_v_fitptr->call_sampler((*__pyx_v_argsptr), (*__py...
                                 ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:150:9: note: 
      candidate template ignored: substitution failure [with propto__ = true,
      jacobian__ = true, T__ = stan::math::var]
    T__ log_prob(vector<T__>& params_r__,
        ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:210:8: note: 
      candidate function template not viable: requires at most 2 arguments, but
      3 were provided
    T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
       ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:343:
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1703:14: error: 
      no matching function for call to 'log_prob_grad'
        lp = stan::model::log_prob_grad<true,true>(model_, par_r, par_i...
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:12138:40: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::log_prob' requested here
    __pyx_t_8 = __pyx_v_self->thisptr->log_prob(__pyx_v_par_r, __pyx_t_6...
                                       ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:77:12: note: 
      candidate template ignored: substitution failure [with propto = true,
      jacobian_adjust_transform = true, M =
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce]
    double log_prob_grad(const M& model,
           ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:168:12: note: 
      candidate function template not viable: requires at most 4 arguments, but
      5 were provided
    double log_prob_grad(const M& model,
           ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:49:28: error: 
      no matching member function for call to 'log_prob'
          = model.template log_prob<true, jacobian_adjust_transform>
            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1694:31: note: 
      in instantiation of function template specialization
      'stan::model::log_prob_propto<true,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
          return stan::model::log_prob_propto<true>(model_, par_r, par_i...
                              ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:12138:40: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::log_prob' requested here
    __pyx_t_8 = __pyx_v_self->thisptr->log_prob(__pyx_v_par_r, __pyx_t_6...
                                       ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:150:9: note: 
      candidate template ignored: substitution failure [with propto__ = true,
      jacobian__ = true, T__ = stan::math::var]
    T__ log_prob(vector<T__>& params_r__,
        ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:210:8: note: 
      candidate function template not viable: requires at most 2 arguments, but
      3 were provided
    T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
       ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:343:
In file included from /Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:18:
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:49:28: error: 
      no matching member function for call to 'log_prob'
          = model.template log_prob<true, jacobian_adjust_transform>
            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1696:31: note: 
      in instantiation of function template specialization
      'stan::model::log_prob_propto<false,
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce>'
      requested here
          return stan::model::log_prob_propto<false>(model_, par_r, par_...
                              ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:12138:40: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::log_prob' requested here
    __pyx_t_8 = __pyx_v_self->thisptr->log_prob(__pyx_v_par_r, __pyx_t_6...
                                       ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:150:9: note: 
      candidate template ignored: substitution failure [with propto__ = true,
      jacobian__ = false, T__ = stan::math::var]
    T__ log_prob(vector<T__>& params_r__,
        ^
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anon_model_44de3e647405f3e3843ab13a390ccfce.hpp:210:8: note: 
      candidate function template not viable: requires at most 2 arguments, but
      3 were provided
    T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
       ^
In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:343:
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan_fit.hpp:1735:9: error: 
      no matching function for call to 'log_prob_grad'
        stan::model::log_prob_grad<true,true>(model_, par_r, par_i, grad...
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccfce_3786978871577808257.cpp:12309:40: note: 
      in instantiation of member function
      'pystan::stan_fit<anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce,
      boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned
      int, 40014, 0, 2147483563>,
      boost::random::linear_congruential_engine<unsigned int, 40692, 0,
      2147483399> > >::grad_log_prob' requested here
    __pyx_t_7 = __pyx_v_self->thisptr->grad_log_prob(__pyx_v_par_r, __pyx_t_6);
                                       ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:77:12: note: 
      candidate template ignored: substitution failure [with propto = true,
      jacobian_adjust_transform = true, M =
      anon_model_44de3e647405f3e3843ab13a390ccfce_namespace::anon_model_44de3e647405f3e3843ab13a390ccfce]
    double log_prob_grad(const M& model,
           ^
/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:168:12: note: 
      candidate function template not viable: requires at most 4 arguments, but
      5 were provided
    double log_prob_grad(const M& model,
           ^
4 warnings and 15 errors generated.
Traceback (most recent call last):
  File "/Users/Nate/anaconda/lib/python3.5/distutils/unixccompiler.py", line 118, in _compile
    extra_postargs)
  File "/Users/Nate/anaconda/lib/python3.5/distutils/ccompiler.py", line 909, in spawn
    spawn(cmd, dry_run=self.dry_run)
  File "/Users/Nate/anaconda/lib/python3.5/distutils/spawn.py", line 36, in spawn
    _spawn_posix(cmd, search_path, dry_run=dry_run)
  File "/Users/Nate/anaconda/lib/python3.5/distutils/spawn.py", line 159, in _spawn_posix
    % (cmd, exit_status))
distutils.errors.DistutilsExecError: command '/usr/bin/clang' failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/model.py", line 310, in __init__
    build_extension.run()
  File "/Users/Nate/anaconda/lib/python3.5/distutils/command/build_ext.py", line 338, in run
    self.build_extensions()
  File "/Users/Nate/anaconda/lib/python3.5/distutils/command/build_ext.py", line 447, in build_extensions
    self._build_extensions_serial()
  File "/Users/Nate/anaconda/lib/python3.5/distutils/command/build_ext.py", line 472, in _build_extensions_serial
    self.build_extension(ext)
  File "/Users/Nate/anaconda/lib/python3.5/distutils/command/build_ext.py", line 532, in build_extension
    depends=ext.depends)
  File "/Users/Nate/anaconda/lib/python3.5/distutils/ccompiler.py", line 574, in compile
    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
  File "/Users/Nate/anaconda/lib/python3.5/distutils/unixccompiler.py", line 120, in _compile
    raise CompileError(msg)
distutils.errors.CompileError: command '/usr/bin/clang' failed with exit status 1

PyStan Version: 2.12.0

Python Version: 3.5.2

Operating System: Mac OS X 10.11.6

ariddell commented 8 years ago

Interesting. Did this happen with PyStan 2.11.0 as well?

I can't reproduce with gcc and PyStan 2.12.0.

It looks like an include error, but that isn't consistent with it working in the other case (the model without alphanumeric characters). For example,

/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:168:12: note: 
      candidate function template not viable: requires at most 4 arguments, but
      5 were provided
    double log_prob_grad(const M& model,
...

looks like it isn't finding the right code.

ariddell commented 8 years ago

Any thoughts @syclik ?

Auerilas commented 8 years ago

I can’t say about 2.11. I was using 2.9 and had this problem shortly after upgrading Xcode, that’s when I tried updating pystan to v2.12 and still had issues.

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 18, 2016, at 6:15 PM, Allen Riddell notifications@github.com wrote:

Interesting. Did this happen with PyStan 2.11.0 as well?

I can't reproduce with gcc and PyStan 2.12.0.

It looks like an include error, but that isn't consistent with it working in the other case (the model without alphanumeric characters). For example,

/Users/Nate/anaconda/lib/python3.5/site-packages/pystan/stan/src/stan/model/util.hpp:168:12: note: candidate function template not viable: requires at most 4 arguments, but 5 were provided double log_prob_grad(const M& model, ... — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stan-dev/pystan/issues/259#issuecomment-247893295, or mute the thread https://github.com/notifications/unsubscribe-auth/AI8CSnvzOS9ANwt261fXmjvai8gceRnxks5qrdQcgaJpZM4KAAc2.

ariddell commented 8 years ago

Thanks. I'll see if I can reproduce this sometime this week.

syclik commented 8 years ago

I completely missed the first error message! It was buried in the output. Here it is:

In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_

q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: expected unqualified-id T__ B0; ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^ In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_ q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: expected unqualified-id double B0 = in__.scalar_constrain(); ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^

I think you're including some sort of other, older copy of Boost somehow. This is the only hit I get on Google that looks relevant is this one:

https://github.com/mapnik/mapnik/issues/2747

The workaround is simple: avoid B0. Looks like you've got something on your system that has that defined as a macro.

The permanent solution: try to figure out if you've installed from somewhere else AND how it's getting included before the include calls to the compiler.

Daniel

On Mon, Sep 19, 2016 at 6:19 AM, Allen Riddell notifications@github.com wrote:

Thanks. I'll see if I can reproduce this sometime this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/pystan/issues/259#issuecomment-247909054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZ_F6w35TsuURtZ_I6Jw1Cystxp3WJWks5qrg1EgaJpZM4KAAc2 .

bob-carpenter commented 8 years ago

Also see this:

https://github.com/randombit/botan/issues/350

I don't even know if this is a Python issue or a Boost issue or just an issue with the new Xcode.

On Sep 19, 2016, at 1:19 AM, Daniel Lee notifications@github.com wrote:

I completely missed the first error message! It was buried in the output. Here it is:

In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_

q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: expected unqualified-id T__ B0; ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^ In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_ q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: expected unqualified-id double B0 = in__.scalar_constrain(); ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^

I think you're including some sort of other, older copy of Boost somehow. This is the only hit I get on Google that looks relevant is this one:

https://github.com/mapnik/mapnik/issues/2747

The workaround is simple: avoid B0. Looks like you've got something on your system that has that defined as a macro.

The permanent solution: try to figure out if you've installed from somewhere else AND how it's getting included before the include calls to the compiler.

Daniel

On Mon, Sep 19, 2016 at 6:19 AM, Allen Riddell notifications@github.com wrote:

Thanks. I'll see if I can reproduce this sometime this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/pystan/issues/259#issuecomment-247909054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZ_F6w35TsuURtZ_I6Jw1Cystxp3WJWks5qrg1EgaJpZM4KAAc2 .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

Auerilas commented 8 years ago

I don’t know if this helps, but it looks like Boost devs are aware of the issue: https://github.com/boostorg/geometry/commit/5fad5e3b7db2f980c13fdf4b07aaad7876f4c364

I just tried to update boost to the latest version using

conda install boost

which installed boost 1.60, but that did not fix the issue. I’m unclear if the fix has been included in Boost 1.61 or if they’re still working on it.

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 18, 2016, at 11:26 PM, Bob Carpenter notifications@github.com wrote:

Also see this:

https://github.com/randombit/botan/issues/350

I don't even know if this is a Python issue or a Boost issue or just an issue with the new Xcode.

  • Bob

On Sep 19, 2016, at 1:19 AM, Daniel Lee notifications@github.com wrote:

I completely missed the first error message! It was buried in the output. Here it is:

In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_

q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: expected unqualified-id T__ B0; ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^ In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_ q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: expected unqualified-id double B0 = in__.scalar_constrain(); ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^

I think you're including some sort of other, older copy of Boost somehow. This is the only hit I get on Google that looks relevant is this one:

https://github.com/mapnik/mapnik/issues/2747

The workaround is simple: avoid B0. Looks like you've got something on your system that has that defined as a macro.

The permanent solution: try to figure out if you've installed from somewhere else AND how it's getting included before the include calls to the compiler.

Daniel

On Mon, Sep 19, 2016 at 6:19 AM, Allen Riddell notifications@github.com wrote:

Thanks. I'll see if I can reproduce this sometime this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/pystan/issues/259#issuecomment-247909054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZ_F6w35TsuURtZ_I6Jw1Cystxp3WJWks5qrg1EgaJpZM4KAAc2 .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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syclik commented 8 years ago

Just so we can track it down, what version of OSX? And compiler version?

Hopefully you're able to work around it by renaming the variable. Thanks for submitting a minimal working example.

Daniel

On Sep 19, 2016, at 6:26 PM, Auerilas notifications@github.com wrote:

I don’t know if this helps, but it looks like Boost devs are aware of the issue: https://github.com/boostorg/geometry/commit/5fad5e3b7db2f980c13fdf4b07aaad7876f4c364

I just tried to update boost to the latest version using

conda install boost

which installed boost 1.60, but that did not fix the issue. I’m unclear if the fix has been included in Boost 1.61 or if they’re still working on it.

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 18, 2016, at 11:26 PM, Bob Carpenter notifications@github.com wrote:

Also see this:

https://github.com/randombit/botan/issues/350

I don't even know if this is a Python issue or a Boost issue or just an issue with the new Xcode.

  • Bob

On Sep 19, 2016, at 1:19 AM, Daniel Lee notifications@github.com wrote:

I completely missed the first error message! It was buried in the output. Here it is:

In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_

q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: expected unqualified-id T__ B0; ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^ In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_ q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: expected unqualified-id double B0 = in__.scalar_constrain(); ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^

I think you're including some sort of other, older copy of Boost somehow. This is the only hit I get on Google that looks relevant is this one:

https://github.com/mapnik/mapnik/issues/2747

The workaround is simple: avoid B0. Looks like you've got something on your system that has that defined as a macro.

The permanent solution: try to figure out if you've installed from somewhere else AND how it's getting included before the include calls to the compiler.

Daniel

On Mon, Sep 19, 2016 at 6:19 AM, Allen Riddell notifications@github.com wrote:

Thanks. I'll see if I can reproduce this sometime this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/pystan/issues/259#issuecomment-247909054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZ_F6w35TsuURtZ_I6Jw1Cystxp3WJWks5qrg1EgaJpZM4KAAc2 .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

Auerilas commented 8 years ago

No worries! I’m on OS X 10.11.6, and heres my clang info:

Nates-Macbook:~ Nate$ clang -v Apple LLVM version 8.0.0 (clang-800.0.38) Target: x86_64-apple-darwin15.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

PyStan works awesome as long as I avoid B0, so I’m still able to keep working in the meantime. It was just an unusual error and I didn’t know how to debug that one.

Thanks again!

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 19, 2016, at 3:02 PM, Daniel Lee notifications@github.com wrote:

Just so we can track it down, what version of OSX? And compiler version?

Hopefully you're able to work around it by renaming the variable. Thanks for submitting a minimal working example.

Daniel

On Sep 19, 2016, at 6:26 PM, Auerilas notifications@github.com wrote:

I don’t know if this helps, but it looks like Boost devs are aware of the issue: https://github.com/boostorg/geometry/commit/5fad5e3b7db2f980c13fdf4b07aaad7876f4c364

I just tried to update boost to the latest version using

conda install boost

which installed boost 1.60, but that did not fix the issue. I’m unclear if the fix has been included in Boost 1.61 or if they’re still working on it.

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 18, 2016, at 11:26 PM, Bob Carpenter notifications@github.com wrote:

Also see this:

https://github.com/randombit/botan/issues/350

I don't even know if this is a Python issue or a Boost issue or just an issue with the new Xcode.

  • Bob

On Sep 19, 2016, at 1:19 AM, Daniel Lee notifications@github.com wrote:

I completely missed the first error message! It was buried in the output. Here it is:

In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_

q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: expected unqualified-id T__ B0; ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^ In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_ q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: expected unqualified-id double B0 = in__.scalar_constrain(); ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^

I think you're including some sort of other, older copy of Boost somehow. This is the only hit I get on Google that looks relevant is this one:

https://github.com/mapnik/mapnik/issues/2747

The workaround is simple: avoid B0. Looks like you've got something on your system that has that defined as a macro.

The permanent solution: try to figure out if you've installed from somewhere else AND how it's getting included before the include calls to the compiler.

Daniel

On Mon, Sep 19, 2016 at 6:19 AM, Allen Riddell notifications@github.com wrote:

Thanks. I'll see if I can reproduce this sometime this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/pystan/issues/259#issuecomment-247909054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZ_F6w35TsuURtZ_I6Jw1Cystxp3WJWks5qrg1EgaJpZM4KAAc2 .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

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bob-carpenter commented 8 years ago

If this is a long-running issue, I can flag it in the Stan parser. But I think it's Boost related and that they know about the problem and will fix it.

On Sep 19, 2016, at 5:21 PM, Auerilas notifications@github.com wrote:

No worries! I’m on OS X 10.11.6, and heres my clang info:

Nates-Macbook:~ Nate$ clang -v Apple LLVM version 8.0.0 (clang-800.0.38) Target: x86_64-apple-darwin15.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

PyStan works awesome as long as I avoid B0, so I’m still able to keep working in the meantime. It was just an unusual error and I didn’t know how to debug that one.

Thanks again!

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 19, 2016, at 3:02 PM, Daniel Lee notifications@github.com wrote:

Just so we can track it down, what version of OSX? And compiler version?

Hopefully you're able to work around it by renaming the variable. Thanks for submitting a minimal working example.

Daniel

On Sep 19, 2016, at 6:26 PM, Auerilas notifications@github.com wrote:

I don’t know if this helps, but it looks like Boost devs are aware of the issue: https://github.com/boostorg/geometry/commit/5fad5e3b7db2f980c13fdf4b07aaad7876f4c364

I just tried to update boost to the latest version using

conda install boost

which installed boost 1.60, but that did not fix the issue. I’m unclear if the fix has been included in Boost 1.61 or if they’re still working on it.

Nathan Lemoine

Research Scientist I USDA NIFA-AFRI Postdoctoral Fellow

Colorado State University Department of Biology Graduate Degree Program in Ecology

On Sep 18, 2016, at 11:26 PM, Bob Carpenter notifications@github.com wrote:

Also see this:

https://github.com/randombit/botan/issues/350

I don't even know if this is a Python issue or a Boost issue or just an issue with the new Xcode.

  • Bob

On Sep 19, 2016, at 1:19 AM, Daniel Lee notifications@github.com wrote:

I completely missed the first error message! It was buried in the output. Here it is:

In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_

q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:163:13: error: expected unqualified-id T__ B0; ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^ In file included from /var/folders/zl/yxc7hlld61b6y2n5ghnn_ q4h0000gn/T/tmpn8_yvo9c/stanfit4anon_model_44de3e647405f3e3843ab13a390ccf ce_3786978871577808257.cpp:345: /var/folders/zl/yxc7hlld61b6y2n5ghnn_q4h0000gn/T/tmpn8_yvo9c/anonmodel 44de3e647405f3e3843ab13a390ccfce.hpp:250:16: error: expected unqualified-id double B0 = in__.scalar_constrain(); ^ /usr/include/sys/termios.h:291:12: note: expanded from macro 'B0'

define B0 0

^

I think you're including some sort of other, older copy of Boost somehow. This is the only hit I get on Google that looks relevant is this one:

https://github.com/mapnik/mapnik/issues/2747

The workaround is simple: avoid B0. Looks like you've got something on your system that has that defined as a macro.

The permanent solution: try to figure out if you've installed from somewhere else AND how it's getting included before the include calls to the compiler.

Daniel

On Mon, Sep 19, 2016 at 6:19 AM, Allen Riddell notifications@github.com wrote:

Thanks. I'll see if I can reproduce this sometime this week.

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ariddell commented 8 years ago

I'm going to close this for now since it's not something that can be fixed in the PyStan code. Thanks for the very detailed report @Auerilas . This is very helpful.