Compiling error

nzgwynn · June 28, 2017, 1:27pm

Hi There,

I am getting this error when I run this stan model - GitHub - nzgwynn/Amelia: Survival Analysis Approach using Stan (amaliaRStan.R and model.stan):

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from filef0543d59b9ee.cpp:8:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /Users/gwynn/Library/R/3.3/library/BH/include/boost/math/tools/config.hpp:13:
In file included from /Users/gwynn/Library/R/3.3/library/BH/include/boost/config.hpp:39:
/Users/gwynn/Library/R/3.3/library/BH/include/boost/config/compil
In addition: Warning message:
running command ‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB filef0543d59b9ee.cpp 2> filef0543d59b9ee.cpp.err.txt’ had status 1

Also:

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rstan_2.15.1 StanHeaders_2.15.0-1 ggplot2_2.2.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 codetools_0.2-15 assertthat_0.1 grid_3.3.2 plyr_1.8.4
[6] gtable_0.2.0 stats4_3.3.2 scales_0.4.1 lazyeval_0.2.0 tools_3.3.2
[11] munsell_0.4.3 parallel_3.3.2 inline_0.3.14 colorspace_1.3-2 gridExtra_2.2.1
[16] tibble_1.2

Does anyone have any suggestions?

Thanks,
gwynn

ekeith · June 28, 2017, 1:51pm

Are you able to succsessfuly run the below code? If not it’s likely an issue with your toolchain, in which case see config notes here.

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
	return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )
fx( 2L, 5 ) # should be 10

nzgwynn · June 28, 2017, 2:03pm

Yes!! I got 10:

fx ← inline::cxxfunction( signature(x = “integer”, y = “numeric” ) , ’

return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
```
                       ' )
```

fx( 2L, 5 )
[1] 10

Will check the link you suggested…

Just to be clear, I should follow the instructions under the Configuration heading which starts with:
“This subsection is optional in the sense that RStan should work without it. Nevertheless, the following is strongly recommended.” Yes???

nzgwynn · June 28, 2017, 3:08pm

I went to the link and ran these two bits of coding:

dotR ← file.path(Sys.getenv(“HOME”), “.R”)
if (!file.exists(dotR)) dir.create(dotR)
M ← file.path(dotR, “Makevars”)
if (!file.exists(M)) file.create(M)
cat(“\nCXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function”,
file = M, sep = “\n”, append = TRUE)

and:

cat(“\nCC=clang”, “CXX=clang++ -arch x86_64 -ftemplate-depth-256”,
file = M, sep = “\n”, append = TRUE)

In addition, I ran this:

cat(readLines(M), sep = “\n”)

CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function

CC=clang
CXX=clang++ -arch x86_64 -ftemplate-depth-256.

I reran the model and got these errors:

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from filef054415fc37f.cpp:8:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /Users/gwynn/Library/R/3.3/library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /Users/gwynn/Library/R/3.3/library/BH/include/boost/math/tools/config.hpp:13:
In file included from /Users/gwynn/Library/R/3.3/library/BH/include/boost/config.hpp:39:
/Users/gwynn/Library/R/3.3/library/BH/include/boost/config/compil
In addition: Warning message:
running command ‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB filef054415fc37f.cpp 2> filef054415fc37f.cpp.err.txt’ had status 1

I have run other survival analysis models by DW Bester that used RStan, but can’t seem to find them to link them.

bgoodri · June 29, 2017, 12:33am

This is a parser bug because the generated C++ code doesn’t compile. @Bob_Carpenter should be able to track it down.

file7f767d87af5.cpp:557:32: error: no matching function for call to 'like'
                lp_accum__.add(like<propto__>(get_base1(TDX,i,"TDX",1), beta, gamma, 0.90000000000000002, 0.80000000000000004, pstream__));
                               ^~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:114:39: note: in instantiation of function template specialization 'model7f73886e2d2_model_namespace::model7f73886e2d2_model::log_prob<false, true, double>' requested here
            log_prob = model.template log_prob<false, true>
                                      ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:54:19: note: in instantiation of function template specialization 'stan::services::util::initialize<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
          = util::initialize(model, init, rng, init_radius,
                  ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:459:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:296:1: note: candidate template ignored: invalid explicitly-specified argument for template parameter 'T0__'
like(const Eigen::Matrix<T0__, Eigen::Dynamic,1>& TDX,
^
file7f767d87af5.cpp:557:32: error: no matching function for call to 'like'
                lp_accum__.add(like<propto__>(get_base1(TDX,i,"TDX",1), beta, gamma, 0.90000000000000002, 0.80000000000000004, pstream__));
                               ^~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:44:28: note: in instantiation of function template specialization 'model7f73886e2d2_model_namespace::model7f73886e2d2_model::log_prob<true, true, stan::math::var>' requested here
          = model.template log_prob<propto, jacobian_adjust_transform>
                           ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:147:37: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
            log_prob = stan::model::log_prob_grad<true, true>
                                    ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:54:19: note: in instantiation of function template specialization 'stan::services::util::initialize<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
          = util::initialize(model, init, rng, init_radius,
                  ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:459:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:296:1: note: candidate template ignored: invalid explicitly-specified argument for template parameter 'T0__'
like(const Eigen::Matrix<T0__, Eigen::Dynamic,1>& TDX,
^
In file included from file7f767d87af5.cpp:720:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:6:
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/finite_diff_grad.hpp:46:21: error: no matching member function for call to 'log_prob'
          .template log_prob<propto,
          ~~~~~~~~~~^~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:62:7: note: in instantiation of function template specialization 'stan::model::finite_diff_grad<false, true, model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
      finite_diff_grad<false, true, Model>(model, interrupt, params_r, params_i,
      ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:61:26: note: in instantiation of function template specialization 'stan::model::test_gradients<true, true, model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
          = stan::model::test_gradients<true, true>(model, cont_vector,
                         ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:459:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:507:9: note: candidate template ignored: substitution failure [with propto__ = false, jacobian__ = true, T__ = double]
    T__ log_prob(vector<T__>& params_r__,
        ^
file7f767d87af5.cpp:575:8: 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 file7f767d87af5.cpp:720:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:6:
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/finite_diff_grad.hpp:52:21: error: no matching member function for call to 'log_prob'
          .template log_prob<propto,
          ~~~~~~~~~~^~~~~~~~~~~~~~~~
file7f767d87af5.cpp:507:9: note: candidate template ignored: substitution failure [with propto__ = false, jacobian__ = true, T__ = double]
    T__ log_prob(vector<T__>& params_r__,
        ^
file7f767d87af5.cpp:575:8: 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,
       ^
file7f767d87af5.cpp:557:32: error: no matching function for call to 'like'
                lp_accum__.add(like<propto__>(get_base1(TDX,i,"TDX",1), beta, gamma, 0.90000000000000002, 0.80000000000000004, pstream__));
                               ^~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:61:31: note: in instantiation of function template specialization 'model7f73886e2d2_model_namespace::model7f73886e2d2_model::log_prob<false, false, double>' requested here
          lp = model.template log_prob<false, false>(cont_vector, disc_vector,
                              ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:480:35: note: in instantiation of function template specialization 'stan::services::optimize::newton<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
      = stan::services::optimize::newton(model, *init_context_ptr,
                                  ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:296:1: note: candidate template ignored: invalid explicitly-specified argument for template parameter 'T0__'
like(const Eigen::Matrix<T0__, Eigen::Dynamic,1>& TDX,
^
file7f767d87af5.cpp:557:32: error: no matching function for call to 'like'
                lp_accum__.add(like<propto__>(get_base1(TDX,i,"TDX",1), beta, gamma, 0.90000000000000002, 0.80000000000000004, pstream__));
                               ^~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:44:28: note: in instantiation of function template specialization 'model7f73886e2d2_model_namespace::model7f73886e2d2_model::log_prob<true, false, stan::math::var>' requested here
          = model.template log_prob<propto, jacobian_adjust_transform>
                           ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/optimization/newton.hpp:66:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, false, model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
            f1 = stan::model::log_prob_grad<true, false>(model,
                              ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:102:36: note: in instantiation of function template specialization 'stan::optimization::newton_step<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
          lp = stan::optimization::newton_step(model, cont_vector, disc_vector);
                                   ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:480:35: note: in instantiation of function template specialization 'stan::services::optimize::newton<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
      = stan::services::optimize::newton(model, *init_context_ptr,
                                  ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:296:1: note: candidate template ignored: invalid explicitly-specified argument for template parameter 'T0__'
like(const Eigen::Matrix<T0__, Eigen::Dynamic,1>& TDX,
^
file7f767d87af5.cpp:582:14: error: no matching member function for call to 'log_prob'
      return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_functional.hpp:23:11: note: in instantiation of function template specialization 'model7f73886e2d2_model_namespace::model7f73886e2d2_model::log_prob<true, true, stan::math::var>' requested here
          log_prob<true, true, T>(const_cast<Eigen::Matrix<T, -1, 1>& >(x), o);
          ^
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/functor/gradient.hpp:51:22: note: in instantiation of function template specialization 'stan::model::model_functional<model7f73886e2d2_model_namespace::model7f73886e2d2_model>::operator()<stan::math::var>' requested here
        var fx_var = f(x_var);
                     ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/gradient.hpp:31:21: note: in instantiation of function template specialization 'stan::math::gradient<stan::model::model_functional<model7f73886e2d2_model_namespace::model7f73886e2d2_model> >' requested here
        stan::math::gradient(model_functional<M>(model, &ss), x, f, grad_f);
                    ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp:69:24: note: in instantiation of function template specialization 'stan::model::gradient<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
          stan::model::gradient(model_, z.q, z.V, z.g, logger);
                       ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp:27:21: note: in instantiation of member function 'stan::mcmc::base_hamiltonian<model7f73886e2d2_model_namespace::model7f73886e2d2_model, stan::mcmc::dense_e_point, 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> > >::update_potential_gradient' requested here
        hamiltonian.update_potential_gradient(z, logger);
                    ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp:14:7: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
      expl_leapfrog()
      ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/sample/hmc_nuts_dense_e.hpp:79:11: note: in instantiation of member function 'stan::mcmc::dense_e_nuts<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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> > >::dense_e_nuts' requested here
          sampler(model, rng);
          ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/sample/hmc_nuts_dense_e.hpp:136:16: note: in instantiation of function template specialization 'stan::services::sample::hmc_nuts_dense_e<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
        return hmc_nuts_dense_e(model, init, unit_e_metric,
               ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:602:13: note: in instantiation of function template specialization 'stan::services::sample::hmc_nuts_dense_e<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
          ::hmc_nuts_dense_e(model, *init_context_ptr,
            ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:507:9: note: candidate template ignored: substitution failure [with propto__ = true, jacobian__ = true, T__ = stan::math::var]
    T__ log_prob(vector<T__>& params_r__,
        ^
file7f767d87af5.cpp:575:8: 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,
       ^
file7f767d87af5.cpp:582:14: error: no matching member function for call to 'log_prob'
      return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/variational/advi.hpp:114:47: note: in instantiation of function template specialization 'model7f73886e2d2_model_namespace::model7f73886e2d2_model::log_prob<false, true, double>' requested here
            double log_prob = model_.template log_prob<false, true>(zeta, &ss);
                                              ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/variational/advi.hpp:200:23: note: in instantiation of member function 'stan::variational::advi<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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, logger);
                      ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/variational/advi.hpp:497:17: note: in instantiation of member function 'stan::variational::advi<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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, logger);
                ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/experimental/advi/fullrank.hpp:85:20: note: in instantiation of member function 'stan::variational::advi<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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,
                   ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:871:9: note: in instantiation of function template specialization 'stan::services::experimental::advi::fullrank<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
      ::fullrank(model, *init_context_ptr,
        ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:507:9: note: candidate template ignored: substitution failure [with propto__ = false, jacobian__ = true, T__ = double]
    T__ log_prob(vector<T__>& params_r__,
        ^
file7f767d87af5.cpp:575:8: 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 file7f767d87af5.cpp:720:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:52:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/experimental/advi/fullrank.hpp:11:
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/variational/advi.hpp:114:47: error: no matching member function for call to 'log_prob'
            double log_prob = model_.template log_prob<false, true>(zeta, &ss);
                              ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/variational/advi.hpp:200:23: note: in instantiation of member function 'stan::variational::advi<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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, logger);
                      ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/variational/advi.hpp:497:17: note: in instantiation of member function 'stan::variational::advi<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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, logger);
                ^
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/experimental/advi/meanfield.hpp:85:20: note: in instantiation of member function 'stan::variational::advi<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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,
                   ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:881:9: note: in instantiation of function template specialization 'stan::services::experimental::advi::meanfield<model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
      ::meanfield(model, *init_context_ptr,
        ^
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1200:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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 = command(args, model_, holder, names_oi_tidx_,
          ^
file7f767d87af5.cpp:731:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::call_sampler)
                                                                                                                   ^
file7f767d87af5.cpp:507:9: note: candidate template ignored: could not match 'vector' against 'Matrix'
    T__ log_prob(vector<T__>& params_r__,
        ^
file7f767d87af5.cpp:575:8: note: candidate template ignored: substitution failure [with propto = false, jacobian = true, T_ = double]
    T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
       ^
In file included from file7f767d87af5.cpp:720:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:36:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/optimize/bfgs.hpp:11:
In file included from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/optimization/bfgs.hpp:5:
/usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/log_prob_propto.hpp:45:28: error: no matching member function for call to 'log_prob'
          = model.template log_prob<true, jacobian_adjust_transform>
            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:1121:40: note: in instantiation of function template specialization 'stan::model::log_prob_propto<true, model7f73886e2d2_model_namespace::model7f73886e2d2_model>' requested here
        return Rcpp::wrap(stan::model::log_prob_propto<true>(model_, par_r, par_i, &rstan::io::rcout));
                                       ^
file7f767d87af5.cpp:749:116: note: in instantiation of member function 'rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, 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
            &rstan::stan_fit<model7f73886e2d2_model_namespace::model7f73886e2d2_model, boost::random::ecuyer1988>::log_prob)
                                                                                                                   ^
file7f767d87af5.cpp:507:9: note: candidate template ignored: substitution failure [with propto__ = true, jacobian__ = true, T__ = stan::math::var]
    T__ log_prob(vector<T__>& params_r__,
        ^
file7f767d87af5.cpp:575:8: 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,
       ^

Bob_Carpenter · June 30, 2017, 10:03pm

That’s definitely a bug. I’m not sure why it’s even parsing in Stan because you should need an _lpdf suffix on like in order to use the ~ notation. I’ll look into it.

I’m moving it to an issue for Stan:

By the way, you don’t have to declare functions before using unless they’re recursive. They have to be declared before they are used.

Bob_Carpenter · July 1, 2017, 2:16am

The problem is in your model. If you change the line with ~ like(...) to read

    target += like(TDX[i], beta, gamma, 0.9, 0.8);

it compiles fine. I don’t know why it was accepting the syntax with ~ without failing and giving you a warning message. I’m going to change the issue filed on this to reflect what it should be and simplify the example.

If you want to use the ~ syntax, you need to use

    TDX[i] ~ like(beta, gamma, 0.9, 0.8);

and define like as like_lpdf. Adding the _lpdf suffix lets Stan know it’s intended to be used like a probability function, so it will make sure it has a real return type and generate all the necessary trimmings for densities in Stan. You can also just use the target += and use it like a function. The end result will be exactly the same.

Thanks for reporting.

nzgwynn · July 1, 2017, 12:15pm

Hi Bob,

Thanks for your support, the model runs now.

I’m a bit confused though as I based my model on one by D.W. Bester: https://github.com/nzgwynn/Amelia/blob/master/mystanmodel.stan, that uses the ~ syntax but not _lpdf or target. I found an error in my coding as the vector TDX should have [3] and not [2] next to it, but don’t suspect that was the issue. I just think you should know, in case there is a bigger issue.

gwynn

Bob_Carpenter · July 2, 2017, 8:18pm

Thanks. The issue is that we should be requiring _lpdf or _lpmf as a suffix on any density or mass function used in sampling notation.

The link you sent uses _log, which is the deprecated syntax from earlier versions of Stan that we’re still supporting. Support for _log suffixes will probably go away in Stan 3 (no idea when it’ll land; we’re still in disagreement about basic interface organization).

nzgwynn · July 3, 2017, 1:08pm

Ahhhhh… Thanks!

swupnil · September 26, 2017, 10:22pm

models.stan (7.1 KB)

Hi, I’m receiving a similar error after updating to Xcode 9. I then tried updating my R and RStan versions, but I’m still seeing this error when I compile the attached model (that had no problem compiling prior to Xcode 9). The only thing I can think is I remember, previously I used to get a warning related to the multi_normal line at the end, but I’m not sure why this error is now appearing instead of the warning:

Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from file72f16fa7330c.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/B
In addition: Warning message:
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file72f16fa7330c.cpp 2> file72f16fa7330c.cpp.err.txt' had status 1

bgoodri · September 27, 2017, 12:45am

If you scroll up through the error messages farther you will see what the problem is. Basically, on line 28, you have

sqrt_Omega_k_ = sqrt(fabs(Omega_k_));

which you need to change to

sqrt_Omega_k_ = sqrt(fabs(Omega_k_ + 0.0));

At any given point in time, about a third of the compilers / compiler versions have ambiguities resolving the versions of the basic functions in the C++ math library, so you often have to give it a hint as to how it should handle things.

swupnil · September 27, 2017, 4:28am

Thanks, Ben. After updating my Rstan and R, and doing this, the model compiles!

Topic		Replies	Views
Unable to compile model General	15	2337	July 23, 2019
Compile error General	7	1675	March 10, 2021
Compiling error General	6	1085	March 9, 2019
Stan compiling error General	6	4147	January 23, 2019
Issue compiling model in rstan General	2	920	October 10, 2017

Compiling error

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