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Stan Model Wont Compile #524

Open y6t4 opened 6 years ago

y6t4 commented 6 years ago

Summary:

I am trying to run my Stan code in an RStudio R Markdown file, but it will not compile and instead produces an error.

Description:

I am trying to run my Stan code in an RStudio R Markdown file, but it will not compile and instead produces an error. I have tried it on two different Mac machines, but the same error is produced.

My code is as follows:

  data{
    int<lower=1> n;  // number of observations
    int<lower=1> p;  // number of predictors
    matrix[n, p] x;  // design matrix
    vector[n] y;     // responses
  }

  transformed data{
    matrix [n, p] Q_ast;
    matrix [p, p] R_ast;
    matrix [p, p] R_ast_inverse;
    Q_ast = qr_Q(x)[,1:p] * sqrt(n-1);
    R_ast = qr_R(x)[1:p,] / sqrt(n-1);
    R_ast_inverse = inverse(R_ast);
  }

  parameters{
    real<lower=-10, upper=10> log_sigma;
    real alpha;      // intercept
    vector[p] theta;  // regression coefficients for predictors
  }

  transformed parameters{
    real sigma;
    vector[p] beta;
    sigma = exp(log_sigma);
    beta = R_ast_inverse * theta; 
  }

  model{
     y  ~ normal(alpha + Q_ast * theta, sigma);
  }

Reproducible Steps:

I simply try to run the aforementioned code.

Current Output:

In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/math/tools/config.hpp:13:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/config.hpp:39:
/usr/local/lib/R/3.5/site-library/BH/include/boost/config/compiler/clang.hpp:200:11: warning: 'BOOST_NO_CXX11_RVALUE_REFERENCES' macro redefined [-Wmacro-redefined]
#  define BOOST_NO_CXX11_RVALUE_REFERENCES
          ^
<command line>:6:9: note: previous definition is here
#define BOOST_NO_CXX11_RVALUE_REFERENCES 1
        ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Core:531:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:36:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/math/constants/constants.hpp:13:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/lexical_cast.hpp:32:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/container/container_fwd.hpp:61:
/usr/local/lib/R/3.5/site-library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/usr/local/lib/R/3.5/site-library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat.hpp:83:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat.hpp:83:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat.hpp:83:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat.hpp:83:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat.hpp:83:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.5/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
filed2ce2cffb55a.cpp:142:228: error: call to 'sqrt' is ambiguous
            stan::math::assign(Q_ast, multiply(stan::model::rvalue(qr_Q(x), stan::model::cons_list(stan::model::index_omni(), stan::model::cons_list(stan::model::index_min_max(1, p), stan::model::nil_index_list())), "qr_Q(x)"),sqrt((n - 1))));
                                                                                                                                                                                                                                   ^~~~
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:970:1: note: candidate function [with _A1 = int]
sqrt(_A1 __lcpp_x) _NOEXCEPT {return ::sqrt((double)__lcpp_x);}
^
/usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/sqrt.hpp:32:5: note: candidate function [with T = int]
    sqrt(const T& x) {
    ^
/usr/include/math.h:447:15: note: candidate function
extern double sqrt(double);
              ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:963:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY float       sqrt(float __lcpp_x) _NOEXCEPT       {return ::sqrtf(__lcpp_x);}
                                             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:964:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long double sqrt(long double __lcpp_x) _NOEXCEPT {return ::sqrtl(__lcpp_x);}
                                             ^
/usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/scal/fun/sqrt.hpp:50:16: note: candidate function
    inline var sqrt(const var& a) {
               ^
filed2ce2cffb55a.cpp:144:226: error: call to 'sqrt' is ambiguous
            stan::math::assign(R_ast, divide(stan::model::rvalue(qr_R(x), stan::model::cons_list(stan::model::index_min_max(1, p), stan::model::cons_list(stan::model::index_omni(), stan::model::nil_index_list())), "qr_R(x)"),sqrt((n - 1))));
                                                                                                                                                                                                                                 ^~~~
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:970:1: note: candidate function [with _A1 = int]
sqrt(_A1 __lcpp_x) _NOEXCEPT {return ::sqrt((double)__lcpp_x);}
^
/usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/prim/mat/fun/sqrt.hpp:32:5: note: candidate function [with T = int]
    sqrt(const T& x) {
    ^
/usr/include/math.h:447:15: note: candidate function
extern double sqrt(double);
              ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:963:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY float       sqrt(float __lcpp_x) _NOEXCEPT       {return ::sqrtf(__lcpp_x);}
                                             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:964:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long double sqrt(long double __lcpp_x) _NOEXCEPT {return ::sqrtl(__lcpp_x);}
                                             ^
/usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/scal/fun/sqrt.hpp:50:16: note: candidate function
    inline var sqrt(const var& a) {
               ^
In file included from filed2ce2cffb55a.cpp:537:
In file included from /usr/local/lib/R/3.5/site-library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /usr/local/lib/R/3.5/site-library/rstan/include/rstan/stan_fit.hpp:36:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/services/optimize/bfgs.hpp:11:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/optimization/bfgs.hpp:9:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/optimization/lbfgs_update.hpp:6:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/circular_buffer.hpp:54:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/circular_buffer/details.hpp:20:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/move/move.hpp:30:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/move/iterator.hpp:27:
/usr/local/lib/R/3.5/site-library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/usr/local/lib/R/3.5/site-library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
16 warnings and 2 errors generated.
make: *** [filed2ce2cffb55a.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:
  1: 
  2: // includes from the plugin
  3: 
  4: 
  5: // user includes
  6: #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.17.0
  7: 
  8: #include <stan/model/model_header.hpp>
  9: 
 10: namespace modeld2ce7662428e_stan_d2ce7301ba1e_namespace {
 11: 
 12: using std::istream;
 13: using std::string;
 14: using std::stringstream;
 15: using std::vector;
 16: using stan::io::dump;
 17: using stan::math::lgamma;
 18: using stan::model::prob_grad;
 19: using namespace stan::math;
 20: 
 21: typedef Eigen::Matrix<double,Eigen::Dynamic,1> vector_d;
 22: typedef Eigen::Matrix<double,1,Eigen::Dynamic> row_vector_d;
 23: typedef Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> matrix_d;
 24: 
 25: static int current_statement_begin__;
 26: 
 27: stan::io::program_reader prog_reader__() {
 28:     stan::io::program_reader reader;
 29:     reader.add_event(0, 0, "start", "modeld2ce7662428e_stan_d2ce7301ba1e");
 30:     reader.add_event(32, 32, "end", "modeld2ce7662428e_stan_d2ce7301ba1e");
 31:     return reader;
 32: }
 33: 
 34: class modeld2ce7662428e_stan_d2ce7301ba1e : public prob_grad {
 35: private:
 36:     int n;
 37:     int p;
 38:     matrix_d x;
 39:     vector_d y;
 40:     matrix_d Q_ast;
 41:     matrix_d R_ast;
 42:     matrix_d R_ast_inverse;
 43: public:
 44:     modeld2ce7662428e_stan_d2ce7301ba1e(stan::io::var_context& context__,
 45:         std::ostream* pstream__ = 0)
 46:         : prob_grad(0) {
 47:         ctor_body(context__, 0, pstream__);
 48:     }
 49: 
 50:     modeld2ce7662428e_stan_d2ce7301ba1e(stan::io::var_context& context__,
 51:         unsigned int random_seed__,
 52:         std::ostream* pstream__ = 0)
 53:         : prob_grad(0) {
 54:         ctor_body(context__, random_seed__, pstream__);
 55:     }
 56: 
 57:     void ctor_body(stan::io::var_context& context__,
 58:                    unsigned int random_seed__,
 59:                    std::ostream* pstream__) {
 60:         boost::ecuyer1988 base_rng__ =
 61:           stan::services::util::create_rng(random_seed__, 0);
 62:         (void) base_rng__;  // suppress unused var warning
 63: 
 64:         current_statement_begin__ = -1;
 65: 
 66:         static const char* function__ = "modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e";
 67:         (void) function__;  // dummy to suppress unused var warning
 68:         size_t pos__;
 69:         (void) pos__;  // dummy to suppress unused var warning
 70:         std::vector<int> vals_i__;
 71:         std::vector<double> vals_r__;
 72:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
 73:         (void) DUMMY_VAR__;  // suppress unused var warning
 74: 
 75:         // initialize member variables
 76:         try {
 77:             current_statement_begin__ = 2;
 78:             context__.validate_dims("data initialization", "n", "int", context__.to_vec());
 79:             n = int(0);
 80:             vals_i__ = context__.vals_i("n");
 81:             pos__ = 0;
 82:             n = vals_i__[pos__++];
 83:             current_statement_begin__ = 3;
 84:             context__.validate_dims("data initialization", "p", "int", context__.to_vec());
 85:             p = int(0);
 86:             vals_i__ = context__.vals_i("p");
 87:             pos__ = 0;
 88:             p = vals_i__[pos__++];
 89:             current_statement_begin__ = 4;
 90:             validate_non_negative_index("x", "n", n);
 91:             validate_non_negative_index("x", "p", p);
 92:             context__.validate_dims("data initialization", "x", "matrix_d", context__.to_vec(n,p));
 93:             validate_non_negative_index("x", "n", n);
 94:             validate_non_negative_index("x", "p", p);
 95:             x = matrix_d(static_cast<Eigen::VectorXd::Index>(n),static_cast<Eigen::VectorXd::Index>(p));
 96:             vals_r__ = context__.vals_r("x");
 97:             pos__ = 0;
 98:             size_t x_m_mat_lim__ = n;
 99:             size_t x_n_mat_lim__ = p;
100:             for (size_t n_mat__ = 0; n_mat__ < x_n_mat_lim__; ++n_mat__) {
101:                 for (size_t m_mat__ = 0; m_mat__ < x_m_mat_lim__; ++m_mat__) {
102:                     x(m_mat__,n_mat__) = vals_r__[pos__++];
103:                 }
104:             }
105:             current_statement_begin__ = 5;
106:             validate_non_negative_index("y", "n", n);
107:             context__.validate_dims("data initialization", "y", "vector_d", context__.to_vec(n));
108:             validate_non_negative_index("y", "n", n);
109:             y = vector_d(static_cast<Eigen::VectorXd::Index>(n));
110:             vals_r__ = context__.vals_r("y");
111:             pos__ = 0;
112:             size_t y_i_vec_lim__ = n;
113:             for (size_t i_vec__ = 0; i_vec__ < y_i_vec_lim__; ++i_vec__) {
114:                 y[i_vec__] = vals_r__[pos__++];
115:             }
116: 
117:             // validate, data variables
118:             current_statement_begin__ = 2;
119:             check_greater_or_equal(function__,"n",n,1);
120:             current_statement_begin__ = 3;
121:             check_greater_or_equal(function__,"p",p,1);
122:             current_statement_begin__ = 4;
123:             current_statement_begin__ = 5;
124:             // initialize data variables
125:             current_statement_begin__ = 9;
126:             validate_non_negative_index("Q_ast", "n", n);
127:             validate_non_negative_index("Q_ast", "p", p);
128:             Q_ast = matrix_d(static_cast<Eigen::VectorXd::Index>(n),static_cast<Eigen::VectorXd::Index>(p));
129:             stan::math::fill(Q_ast,DUMMY_VAR__);
130:             current_statement_begin__ = 10;
131:             validate_non_negative_index("R_ast", "p", p);
132:             validate_non_negative_index("R_ast", "p", p);
133:             R_ast = matrix_d(static_cast<Eigen::VectorXd::Index>(p),static_cast<Eigen::VectorXd::Index>(p));
134:             stan::math::fill(R_ast,DUMMY_VAR__);
135:             current_statement_begin__ = 11;
136:             validate_non_negative_index("R_ast_inverse", "p", p);
137:             validate_non_negative_index("R_ast_inverse", "p", p);
138:             R_ast_inverse = matrix_d(static_cast<Eigen::VectorXd::Index>(p),static_cast<Eigen::VectorXd::Index>(p));
139:             stan::math::fill(R_ast_inverse,DUMMY_VAR__);
140: 
141:             current_statement_begin__ = 12;
142:             stan::math::assign(Q_ast, multiply(stan::model::rvalue(qr_Q(x), stan::model::cons_list(stan::model::index_omni(), stan::model::cons_list(stan::model::index_min_max(1, p), stan::model::nil_index_list())), "qr_Q(x)"),sqrt((n - 1))));
143:             current_statement_begin__ = 13;
144:             stan::math::assign(R_ast, divide(stan::model::rvalue(qr_R(x), stan::model::cons_list(stan::model::index_min_max(1, p), stan::model::cons_list(stan::model::index_omni(), stan::model::nil_index_list())), "qr_R(x)"),sqrt((n - 1))));
145:             current_statement_begin__ = 14;
146:             stan::math::assign(R_ast_inverse, inverse(R_ast));
147: 
148:             // validate transformed data
149:             current_statement_begin__ = 9;
150:             current_statement_begin__ = 10;
151:             current_statement_begin__ = 11;
152: 
153:             // validate, set parameter ranges
154:             num_params_r__ = 0U;
155:             param_ranges_i__.clear();
156:             current_statement_begin__ = 18;
157:             ++num_params_r__;
158:             current_statement_begin__ = 19;
159:             ++num_params_r__;
160:             current_statement_begin__ = 20;
161:             validate_non_negative_index("theta", "p", p);
162:             num_params_r__ += p;
163:         } catch (const std::exception& e) {
164:             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
165:             // Next line prevents compiler griping about no return
166:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
167:         }
168:     }
169: 
170:     ~modeld2ce7662428e_stan_d2ce7301ba1e() { }
171: 
172: 
173:     void transform_inits(const stan::io::var_context& context__,
174:                          std::vector<int>& params_i__,
175:                          std::vector<double>& params_r__,
176:                          std::ostream* pstream__) const {
177:         stan::io::writer<double> writer__(params_r__,params_i__);
178:         size_t pos__;
179:         (void) pos__; // dummy call to supress warning
180:         std::vector<double> vals_r__;
181:         std::vector<int> vals_i__;
182: 
183:         if (!(context__.contains_r("log_sigma")))
184:             throw std::runtime_error("variable log_sigma missing");
185:         vals_r__ = context__.vals_r("log_sigma");
186:         pos__ = 0U;
187:         context__.validate_dims("initialization", "log_sigma", "double", context__.to_vec());
188:         double log_sigma(0);
189:         log_sigma = vals_r__[pos__++];
190:         try {
191:             writer__.scalar_lub_unconstrain(-(10),10,log_sigma);
192:         } catch (const std::exception& e) { 
193:             throw std::runtime_error(std::string("Error transforming variable log_sigma: ") + e.what());
194:         }
195: 
196:         if (!(context__.contains_r("alpha")))
197:             throw std::runtime_error("variable alpha missing");
198:         vals_r__ = context__.vals_r("alpha");
199:         pos__ = 0U;
200:         context__.validate_dims("initialization", "alpha", "double", context__.to_vec());
201:         double alpha(0);
202:         alpha = vals_r__[pos__++];
203:         try {
204:             writer__.scalar_unconstrain(alpha);
205:         } catch (const std::exception& e) { 
206:             throw std::runtime_error(std::string("Error transforming variable alpha: ") + e.what());
207:         }
208: 
209:         if (!(context__.contains_r("theta")))
210:             throw std::runtime_error("variable theta missing");
211:         vals_r__ = context__.vals_r("theta");
212:         pos__ = 0U;
213:         validate_non_negative_index("theta", "p", p);
214:         context__.validate_dims("initialization", "theta", "vector_d", context__.to_vec(p));
215:         vector_d theta(static_cast<Eigen::VectorXd::Index>(p));
216:         for (int j1__ = 0U; j1__ < p; ++j1__)
217:             theta(j1__) = vals_r__[pos__++];
218:         try {
219:             writer__.vector_unconstrain(theta);
220:         } catch (const std::exception& e) { 
221:             throw std::runtime_error(std::string("Error transforming variable theta: ") + e.what());
222:         }
223: 
224:         params_r__ = writer__.data_r();
225:         params_i__ = writer__.data_i();
226:     }
227: 
228:     void transform_inits(const stan::io::var_context& context,
229:                          Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
230:                          std::ostream* pstream__) const {
231:       std::vector<double> params_r_vec;
232:       std::vector<int> params_i_vec;
233:       transform_inits(context, params_i_vec, params_r_vec, pstream__);
234:       params_r.resize(params_r_vec.size());
235:       for (int i = 0; i < params_r.size(); ++i)
236:         params_r(i) = params_r_vec[i];
237:     }
238: 
239: 
240:     template <bool propto__, bool jacobian__, typename T__>
241:     T__ log_prob(vector<T__>& params_r__,
242:                  vector<int>& params_i__,
243:                  std::ostream* pstream__ = 0) const {
244: 
245:         T__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
246:         (void) DUMMY_VAR__;  // suppress unused var warning
247: 
248:         T__ lp__(0.0);
249:         stan::math::accumulator<T__> lp_accum__;
250: 
251:         try {
252:             // model parameters
253:             stan::io::reader<T__> in__(params_r__,params_i__);
254: 
255:             T__ log_sigma;
256:             (void) log_sigma;  // dummy to suppress unused var warning
257:             if (jacobian__)
258:                 log_sigma = in__.scalar_lub_constrain(-(10),10,lp__);
259:             else
260:                 log_sigma = in__.scalar_lub_constrain(-(10),10);
261: 
262:             T__ alpha;
263:             (void) alpha;  // dummy to suppress unused var warning
264:             if (jacobian__)
265:                 alpha = in__.scalar_constrain(lp__);
266:             else
267:                 alpha = in__.scalar_constrain();
268: 
269:             Eigen::Matrix<T__,Eigen::Dynamic,1>  theta;
270:             (void) theta;  // dummy to suppress unused var warning
271:             if (jacobian__)
272:                 theta = in__.vector_constrain(p,lp__);
273:             else
274:                 theta = in__.vector_constrain(p);
275: 
276: 
277:             // transformed parameters
278:             current_statement_begin__ = 24;
279:             T__ sigma;
280:             (void) sigma;  // dummy to suppress unused var warning
281: 
282:             stan::math::initialize(sigma, DUMMY_VAR__);
283:             stan::math::fill(sigma,DUMMY_VAR__);
284:             current_statement_begin__ = 25;
285:             validate_non_negative_index("beta", "p", p);
286:             Eigen::Matrix<T__,Eigen::Dynamic,1>  beta(static_cast<Eigen::VectorXd::Index>(p));
287:             (void) beta;  // dummy to suppress unused var warning
288: 
289:             stan::math::initialize(beta, DUMMY_VAR__);
290:             stan::math::fill(beta,DUMMY_VAR__);
291: 
292: 
293:             current_statement_begin__ = 26;
294:             stan::math::assign(sigma, exp(log_sigma));
295:             current_statement_begin__ = 27;
296:             stan::math::assign(beta, multiply(R_ast_inverse,theta));
297: 
298:             // validate transformed parameters
299:             if (stan::math::is_uninitialized(sigma)) {
300:                 std::stringstream msg__;
301:                 msg__ << "Undefined transformed parameter: sigma";
302:                 throw std::runtime_error(msg__.str());
303:             }
304:             for (int i0__ = 0; i0__ < p; ++i0__) {
305:                 if (stan::math::is_uninitialized(beta(i0__))) {
306:                     std::stringstream msg__;
307:                     msg__ << "Undefined transformed parameter: beta" << '[' << i0__ << ']';
308:                     throw std::runtime_error(msg__.str());
309:                 }
310:             }
311: 
312:             const char* function__ = "validate transformed params";
313:             (void) function__;  // dummy to suppress unused var warning
314:             current_statement_begin__ = 24;
315:             current_statement_begin__ = 25;
316: 
317:             // model body
318: 
319:             current_statement_begin__ = 31;
320:             lp_accum__.add(normal_log<propto__>(y, add(alpha,multiply(Q_ast,theta)), sigma));
321: 
322:         } catch (const std::exception& e) {
323:             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
324:             // Next line prevents compiler griping about no return
325:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
326:         }
327: 
328:         lp_accum__.add(lp__);
329:         return lp_accum__.sum();
330: 
331:     } // log_prob()
332: 
333:     template <bool propto, bool jacobian, typename T_>
334:     T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
335:                std::ostream* pstream = 0) const {
336:       std::vector<T_> vec_params_r;
337:       vec_params_r.reserve(params_r.size());
338:       for (int i = 0; i < params_r.size(); ++i)
339:         vec_params_r.push_back(params_r(i));
340:       std::vector<int> vec_params_i;
341:       return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
342:     }
343: 
344: 
345:     void get_param_names(std::vector<std::string>& names__) const {
346:         names__.resize(0);
347:         names__.push_back("log_sigma");
348:         names__.push_back("alpha");
349:         names__.push_back("theta");
350:         names__.push_back("sigma");
351:         names__.push_back("beta");
352:     }
353: 
354: 
355:     void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
356:         dimss__.resize(0);
357:         std::vector<size_t> dims__;
358:         dims__.resize(0);
359:         dimss__.push_back(dims__);
360:         dims__.resize(0);
361:         dimss__.push_back(dims__);
362:         dims__.resize(0);
363:         dims__.push_back(p);
364:         dimss__.push_back(dims__);
365:         dims__.resize(0);
366:         dimss__.push_back(dims__);
367:         dims__.resize(0);
368:         dims__.push_back(p);
369:         dimss__.push_back(dims__);
370:     }
371: 
372:     template <typename RNG>
373:     void write_array(RNG& base_rng__,
374:                      std::vector<double>& params_r__,
375:                      std::vector<int>& params_i__,
376:                      std::vector<double>& vars__,
377:                      bool include_tparams__ = true,
378:                      bool include_gqs__ = true,
379:                      std::ostream* pstream__ = 0) const {
380:         vars__.resize(0);
381:         stan::io::reader<double> in__(params_r__,params_i__);
382:         static const char* function__ = "modeld2ce7662428e_stan_d2ce7301ba1e_namespace::write_array";
383:         (void) function__;  // dummy to suppress unused var warning
384:         // read-transform, write parameters
385:         double log_sigma = in__.scalar_lub_constrain(-(10),10);
386:         double alpha = in__.scalar_constrain();
387:         vector_d theta = in__.vector_constrain(p);
388:         vars__.push_back(log_sigma);
389:         vars__.push_back(alpha);
390:             for (int k_0__ = 0; k_0__ < p; ++k_0__) {
391:             vars__.push_back(theta[k_0__]);
392:             }
393: 
394:         if (!include_tparams__) return;
395:         // declare and define transformed parameters
396:         double lp__ = 0.0;
397:         (void) lp__;  // dummy to suppress unused var warning
398:         stan::math::accumulator<double> lp_accum__;
399: 
400:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
401:         (void) DUMMY_VAR__;  // suppress unused var warning
402: 
403:         try {
404:             current_statement_begin__ = 24;
405:             double sigma(0.0);
406:             (void) sigma;  // dummy to suppress unused var warning
407: 
408:             stan::math::initialize(sigma, std::numeric_limits<double>::quiet_NaN());
409:             stan::math::fill(sigma,DUMMY_VAR__);
410:             current_statement_begin__ = 25;
411:             validate_non_negative_index("beta", "p", p);
412:             vector_d beta(static_cast<Eigen::VectorXd::Index>(p));
413:             (void) beta;  // dummy to suppress unused var warning
414: 
415:             stan::math::initialize(beta, std::numeric_limits<double>::quiet_NaN());
416:             stan::math::fill(beta,DUMMY_VAR__);
417: 
418: 
419:             current_statement_begin__ = 26;
420:             stan::math::assign(sigma, exp(log_sigma));
421:             current_statement_begin__ = 27;
422:             stan::math::assign(beta, multiply(R_ast_inverse,theta));
423: 
424:             // validate transformed parameters
425:             current_statement_begin__ = 24;
426:             current_statement_begin__ = 25;
427: 
428:             // write transformed parameters
429:         vars__.push_back(sigma);
430:             for (int k_0__ = 0; k_0__ < p; ++k_0__) {
431:             vars__.push_back(beta[k_0__]);
432:             }
433: 
434:             if (!include_gqs__) return;
435:             // declare and define generated quantities
436: 
437: 
438: 
439:             // validate generated quantities
440: 
441:             // write generated quantities
442:         } catch (const std::exception& e) {
443:             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
444:             // Next line prevents compiler griping about no return
445:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
446:         }
447:     }
448: 
449:     template <typename RNG>
450:     void write_array(RNG& base_rng,
451:                      Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
452:                      Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
453:                      bool include_tparams = true,
454:                      bool include_gqs = true,
455:                      std::ostream* pstream = 0) const {
456:       std::vector<double> params_r_vec(params_r.size());
457:       for (int i = 0; i < params_r.size(); ++i)
458:         params_r_vec[i] = params_r(i);
459:       std::vector<double> vars_vec;
460:       std::vector<int> params_i_vec;
461:       write_array(base_rng,params_r_vec,params_i_vec,vars_vec,include_tparams,include_gqs,pstream);
462:       vars.resize(vars_vec.size());
463:       for (int i = 0; i < vars.size(); ++i)
464:         vars(i) = vars_vec[i];
465:     }
466: 
467:     static std::string model_name() {
468:         return "modeld2ce7662428e_stan_d2ce7301ba1e";
469:     }
470: 
471: 
472:     void constrained_param_names(std::vector<std::string>& param_names__,
473:                                  bool include_tparams__ = true,
474:                                  bool include_gqs__ = true) const {
475:         std::stringstream param_name_stream__;
476:         param_name_stream__.str(std::string());
477:         param_name_stream__ << "log_sigma";
478:         param_names__.push_back(param_name_stream__.str());
479:         param_name_stream__.str(std::string());
480:         param_name_stream__ << "alpha";
481:         param_names__.push_back(param_name_stream__.str());
482:         for (int k_0__ = 1; k_0__ <= p; ++k_0__) {
483:             param_name_stream__.str(std::string());
484:             param_name_stream__ << "theta" << '.' << k_0__;
485:             param_names__.push_back(param_name_stream__.str());
486:         }
487: 
488:         if (!include_gqs__ && !include_tparams__) return;
489:         param_name_stream__.str(std::string());
490:         param_name_stream__ << "sigma";
491:         param_names__.push_back(param_name_stream__.str());
492:         for (int k_0__ = 1; k_0__ <= p; ++k_0__) {
493:             param_name_stream__.str(std::string());
494:             param_name_stream__ << "beta" << '.' << k_0__;
495:             param_names__.push_back(param_name_stream__.str());
496:         }
497: 
498:         if (!include_gqs__) return;
499:     }
500: 
501: 
502:     void unconstrained_param_names(std::vector<std::string>& param_names__,
503:                                    bool include_tparams__ = true,
504:                                    bool include_gqs__ = true) const {
505:         std::stringstream param_name_stream__;
506:         param_name_stream__.str(std::string());
507:         param_name_stream__ << "log_sigma";
508:         param_names__.push_back(param_name_stream__.str());
509:         param_name_stream__.str(std::string());
510:         param_name_stream__ << "alpha";
511:         param_names__.push_back(param_name_stream__.str());
512:         for (int k_0__ = 1; k_0__ <= p; ++k_0__) {
513:             param_name_stream__.str(std::string());
514:             param_name_stream__ << "theta" << '.' << k_0__;
515:             param_names__.push_back(param_name_stream__.str());
516:         }
517: 
518:         if (!include_gqs__ && !include_tparams__) return;
519:         param_name_stream__.str(std::string());
520:         param_name_stream__ << "sigma";
521:         param_names__.push_back(param_name_stream__.str());
522:         for (int k_0__ = 1; k_0__ <= p; ++k_0__) {
523:             param_name_stream__.str(std::string());
524:             param_name_stream__ << "beta" << '.' << k_0__;
525:             param_names__.push_back(param_name_stream__.str());
526:         }
527: 
528:         if (!include_gqs__) return;
529:     }
530: 
531: }; // model
532: 
533: }
534: 
535: typedef modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e stan_model;
536: 
537: #include <rstan/rstaninc.hpp>
538: /**
539:  * Define Rcpp Module to expose stan_fit's functions to R.
540:  */
541: RCPP_MODULE(stan_fit4modeld2ce7662428e_stan_d2ce7301ba1e_mod){
542:   Rcpp::class_<rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e,
543:                boost::random::ecuyer1988> >("stan_fit4modeld2ce7662428e_stan_d2ce7301ba1e")
544:     // .constructor<Rcpp::List>()
545:     .constructor<SEXP, SEXP, SEXP>()
546:     // .constructor<SEXP, SEXP>()
547:     .method("call_sampler",
548:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::call_sampler)
549:     .method("param_names",
550:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::param_names)
551:     .method("param_names_oi",
552:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::param_names_oi)
553:     .method("param_fnames_oi",
554:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::param_fnames_oi)
555:     .method("param_dims",
556:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::param_dims)
557:     .method("param_dims_oi",
558:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::param_dims_oi)
559:     .method("update_param_oi",
560:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::update_param_oi)
561:     .method("param_oi_tidx",
562:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::param_oi_tidx)
563:     .method("grad_log_prob",
564:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::grad_log_prob)
565:     .method("log_prob",
566:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::log_prob)
567:     .method("unconstrain_pars",
568:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::unconstrain_pars)
569:     .method("constrain_pars",
570:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::constrain_pars)
571:     .method("num_pars_unconstrained",
572:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::num_pars_unconstrained)
573:     .method("unconstrained_param_names",
574:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::unconstrained_param_names)
575:     .method("constrained_param_names",
576:             &rstan::stan_fit<modeld2ce7662428e_stan_d2ce7301ba1e_namespace::modeld2ce7662428e_stan_d2ce7301ba1e, boost::random::ecuyer1988>::constrained_param_names)
577:     ;
578: }
579: 
580: // declarations
581: extern "C" {
582: SEXP filed2ce2cffb55a( ) ;
583: }
584: 
585: // definition
586: 
587: SEXP filed2ce2cffb55a(  ){
588:  return Rcpp::wrap("stan-d2ce7301ba1e");
589: }
590: 
591: 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/math/tools/config.hpp:13:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/config.hpp:39:
/usr/local/lib/R/3.5/site-library/BH/include/boost/config/compiler/clang.
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command '/usr/local/Cellar/r/3.5.0/lib/R/bin/R CMD SHLIB filed2ce2cffb55a.cpp 2> filed2ce2cffb55a.cpp.err.txt' had status 1
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from filed2ce2cffb55a.cpp:8:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /usr/local/lib/R/3.5/site-library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/math/tools/config.hpp:13:
In file included from /usr/local/lib/R/3.5/site-library/BH/include/boost/config.hpp:39:
/usr/local/lib/R/3.5/site-library/BH/include/boost/config/compiler/clang.

Expected Output:

I expect for the code to compile with the usual warnings.

RStan Version:

2.17.3

R Version:

"R version 3.5.0 (2018-04-23)"

Operating System:

macOS High Sierra 10.13.3

Session Info

R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin17.5.0 (64-bit) Running under: macOS High Sierra 10.13.3

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale: removed

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

other attached packages: [1] StanHeaders_2.17.2

loaded via a namespace (and not attached): [1] Rcpp_0.12.16 knitr_1.20 devtools_1.13.5 munsell_0.4.3
[5] colorspace_1.3-2 lattice_0.20-35 R6_2.2.2 rlang_0.2.0
[9] httr_1.3.1 plyr_1.8.4 tools_3.5.0 parallel_3.5.0
[13] grid_3.5.0 gtable_0.2.0 loo_2.0.0 git2r_0.21.0
[17] withr_2.1.2 matrixStats_0.53.1 lazyeval_0.2.1 digest_0.6.15
[21] tibble_1.4.2 rstan_2.17.3 Matrix_1.2-14 gridExtra_2.3
[25] ggplot2_2.2.1 curl_3.2 memoise_1.1.0 inline_0.3.14
[29] pillar_1.2.2 compiler_3.5.0 scales_0.5.0 stats4_3.5.0

y6t4 commented 6 years ago

I tried to go through the installation instructions again by following this page. I installed the macOS R toolchain using the macOS R toolchain installer.

I then configured clang++ in admin mode using the provided code:

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
MAKEVARS <- file.path(dotR, "Makevars")
if (!file.exists(MAKEVARS)) file.create(MAKEVARS)

cat(
  "\nCXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas",
  "\nCC=clang",
  "CXX=clang++ -arch x86_64 -ftemplate-depth-256",
  file = MAKEVARS, 
  sep = "\n", 
  append = TRUE
)

# print the contents to the console 
cat(readLines(MAKEVARS), sep = "\n")

I then attempt to verify that the toolchain works by executing the code below in R and checking that it returns the value 10:

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
    return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )

fx( 2L, 5 ) # should be 10

But I get the following error:

Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! ld: library not found for -lintl clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [filee7df6bc649.so] Error 1 In addition: Warning message: In system(cmd, intern = !verbose) : running command '/usr/local/Cellar/r/3.5.0/lib/R/bin/R CMD SHLIB filee7df6bc649.cpp 2> filee7df6bc649.cpp.err.txt' had status 1

I think this might be connected to my problem with the Stan model?

bgoodri commented 6 years ago

For the original question, you need to write / sqrt(n - 1.0) with some compilers in order to force it to use the double-based implementation of the square root function.

y6t4 commented 6 years ago

@bgoodri I still get the same error.

bgoodri commented 6 years ago

Which error? You fixed the -lintl thing, changed your Stan program to do / sqrt(n - 1.0);, and it still gives you a compiler error about sqrt being ambiguous?

On Fri, May 11, 2018 at 9:30 AM, y6t4 notifications@github.com wrote:

@bgoodri https://github.com/bgoodri I still get the same error.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/524#issuecomment-388364069, or mute the thread https://github.com/notifications/unsubscribe-auth/ADOrqjVa9xXJCdtFUQp0y_p2lHAo1fA8ks5txZKHgaJpZM4T60On .

y6t4 commented 6 years ago

@bgoodri My apologies. I tried to respond to your comment on the Stan forum, but It said that my post was awaiting review.

How would I go about fixing the -lintl thing?

The output from cat(readLines(MAKEVARS), sep = "\n") is as follows:

> cat(readLines(MAKEVARS), sep = "\n")

# The following statements are required to use the clang4 binary
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
CXX1X=/usr/local/clang4/bin/clang++
CXX98=/usr/local/clang4/bin/clang++
CXX11=/usr/local/clang4/bin/clang++
CXX14=/usr/local/clang4/bin/clang++
CXX17=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
# End clang4 inclusion statements
# The following statement changes the Fortran linking path
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
# End Fortran linking path statement

CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas

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

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

CXXFLAGS+=-flto -Wno-unused-local-typedefs

CXXFLAGS += -Wno-ignored-attributes -Wno-deprecated-declarations
bgoodri commented 6 years ago

Start by deleting everything after

End Fortran linking path statement

On Fri, May 11, 2018 at 9:40 AM, y6t4 notifications@github.com wrote:

@bgoodri https://github.com/bgoodri My apologies. I tried to respond to your comment on the Stan forum, but It said that my post was awaiting review.

How would I go about fixing the -lintl thing?

The output from cat(readLines(MAKEVARS), sep = "\n") is as follows:

cat(readLines(MAKEVARS), sep = "\n")

The following statements are required to use the clang4 binary

CC=/usr/local/clang4/bin/clang CXX=/usr/local/clang4/bin/clang++ CXX1X=/usr/local/clang4/bin/clang++ CXX98=/usr/local/clang4/bin/clang++ CXX11=/usr/local/clang4/bin/clang++ CXX14=/usr/local/clang4/bin/clang++ CXX17=/usr/local/clang4/bin/clang++ LDFLAGS=-L/usr/local/clang4/lib End clang4 inclusion statements The following statement changes the Fortran linking path

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 End Fortran linking path statement

CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -Wno-unknown-pragmas

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

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

CXXFLAGS+=-flto -Wno-unused-local-typedefs

CXXFLAGS += -Wno-ignored-attributes -Wno-deprecated-declarations

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y6t4 commented 6 years ago

@bgoodri

I made the hidden files visible and tried to edit the Makevars file. I get the following error when I try to save the changes:

You don’t own the file “Makevars” and don’t have permission to write to it.

bob-carpenter commented 6 years ago

This Stan program compiles and links for me in the latest RStan on Mac OS X.

bgoodri commented 6 years ago

@y6t4 Just do File -> Open in RStudio and browse to your home directory, then the .R subdirectory (which is possibly hidden), and then the Makevars file.

On Fri, May 11, 2018 at 10:01 AM, Bob Carpenter notifications@github.com wrote:

This Stan program compiles and links for me in the latest RStan on Mac OS X for me.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/524#issuecomment-388372577, or mute the thread https://github.com/notifications/unsubscribe-auth/ADOrqq6hmRtFuYrpNG4e2Ybn28TkaEHtks5txZmzgaJpZM4T60On .

y6t4 commented 6 years ago

@bgoodri IT WORKED! Thank you so much for taking the time to help!!!!!! THANK YOU!