Rstan on Windows

Yeah emptying the Makevars file is a good idea when troubleshooting, but now that it’s working I suggest adding just this line

to Makevars which should make Stan a decent bit faster.

Anyway, glad it’s not crashing at the moment. And if you give CmdStanR a try let us know if you run into any trouble.

Hi everyone,

I just updated R and rstan yesterday. One of my models that was running fine the day before is not running anymore. I get the next error and warning messages:

Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  '-E' not found
2: In system(cmd, intern = !verbose) :
  running command 'C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB fileba824601f4c.cpp 2> fileba824601f4c.cpp.err.txt' had status 1
3: In file(con, "r") :
  cannot open file 'fileba824601f4c.cpp.err.txt': No such file or directory
Error in sink(type = "output") : invalid connection

I am running on widows and using :
R version 4.0.2
Platform x86_64-w64-mingw32/x64 (64-bit)
rstan 2.21.2

I did double check that the model is in the right working directory and I tried with one of the examples form the Stan manual. I get the same error and warning messages.

Any ideas?

Cheers,
Alfonso

I’m having a similar issue with rstan.
session

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] rstan_2.21.2         ggplot2_3.3.2        StanHeaders_2.21.0-5

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         compiler_4.0.2     pillar_1.4.6       prettyunits_1.1.1  tools_4.0.2       
 [6] pkgbuild_1.1.0     jsonlite_1.7.0     lifecycle_0.2.0    tibble_3.0.3       gtable_0.3.0      
[11] pkgconfig_2.0.3    rlang_0.4.7        cli_2.0.2          rstudioapi_0.11    parallel_4.0.2    
[16] curl_4.3           loo_2.3.1          gridExtra_2.3      dplyr_1.0.1        withr_2.2.0       
[21] generics_0.0.2     vctrs_0.3.2        tidyselect_1.1.0   stats4_4.0.2       grid_4.0.2        
[26] glue_1.4.1         inline_0.3.15      R6_2.4.1           processx_3.4.3     fansi_0.4.1       
[31] purrr_0.3.4        callr_3.4.3        magrittr_1.5       codetools_0.2-16   matrixStats_0.56.0
[36] scales_1.1.1       ps_1.3.3           ellipsis_0.3.1     assertthat_0.2.1   colorspace_1.4-1  
[41] V8_3.2.0           RcppParallel_5.0.2 munsell_0.5.0      crayon_1.3.4  

error message when I run

example(stan_model, package = "rstan", run.dontrun = TRUE)
Compilation argument:
 C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB file76b056351fea.cpp 2> file76b056351fea.cpp.err.txt 
"C:/rtools40/mingw64/bin/"g++  -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG   -I"C:/Program Files/R/R-4.0.2/library/Rcpp/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppEigen/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppEigen/include/unsupported"  -I"C:/Program Files/R/R-4.0.2/library/BH/include" -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src/"  -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppParallel/include/"  -I"C:/Program Files/R/R-4.0.2/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include "C:/Program Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp"  -std=c++1y       -include C:/Program Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I "C:/Program Files/R/R-4.0.2/library/StanHeaders/include" -I "C:/Program Files/R/R-4.0.2/library/RcppEigen/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file76b056351fea.cpp -o file76b056351fea.o
g++.exe: error: Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file76b056351fea.o] Error 1
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
2: In file(con, "r") :
  cannot open file 'file76b056351fea.cpp.err.txt': No such file or directory

Makevars

CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
CXX14 = C:/rtools40/mingw64/bin/g++

also tried, same error

CXX14 = C:/rtools40/mingw$(WIN)/bin/g++
and
CXX14 = C:/rtools40/usr/mingw_$(WIN)/bin/g++

What about if you set

CXX14 = C:/rtools40/mingw64/bin/g++

or

CXX14 = C:/rtools40/mingw_64/bin/g++

Though I think the former is the correct one, at least on two Windows machine I have Rtools 4.0 installed.

that’s what I have in makevars

CXX14 = C:/rtools40/mingw64/bin/g++

and checking the folder

1 Like

Can you try stan_demo(1)? If that doesn’t work, your error looks like this thread. Can you try the stuff in that thread?

@spinkney can you reinstall StanHeaders?

This looks like the error: “g++.exe: error: Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory”

1 Like

I did

remove.packages("StanHeaders")

restarted R

Restarting R session...

> install.packages("StanHeaders")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/StanHeaders_2.21.0-5.zip'
Content type 'application/zip' length 2354610 bytes (2.2 MB)
downloaded 2.2 MB

package ‘StanHeaders’ successfully unpacked and MD5 sums checked

Same error

> example(stan_model, package = "rstan", run.dontrun = TRUE)

stn_md> stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}'

stn_md> mod <- stan_model(model_code = stancode, verbose = TRUE)

TRANSLATING MODEL '73fc79f8b1915e8208c736914c86d1a1' FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model '73fc79f8b1915e8208c736914c86d1a1'.
COMPILING THE C++ CODE FOR MODEL '73fc79f8b1915e8208c736914c86d1a1' NOW.
OS: x86_64, mingw32; rstan: 2.21.2; Rcpp: 1.0.5; inline: 0.3.15 
 >> setting environment variables: 
LOCAL_LIBS =  "C:/Program Files/R/R-4.0.2/library/rstan/lib/x64/libStanServices.a" -L"C:/Program Files/R/R-4.0.2/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Program Files/R/R-4.0.2/library/RcppParallel/lib/x64" -ltbb
PKG_CPPFLAGS =   -I"C:/Program Files/R/R-4.0.2/library/Rcpp/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppEigen/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppEigen/include/unsupported"  -I"C:/Program Files/R/R-4.0.2/library/BH/include" -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src/"  -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppParallel/include/"  -I"C:/Program Files/R/R-4.0.2/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include "C:/Program Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp"  -std=c++1y
 >> Program source :

   1 : 
   2 : // includes from the plugin
   3 : // [[Rcpp::plugins(cpp14)]]
   4 : 
   5 : 
   6 : // user includes
   7 : #include <Rcpp.h>
   8 : #include <rstan/io/rlist_ref_var_context.hpp>
   9 : #include <rstan/io/r_ostream.hpp>
  10 : #include <rstan/stan_args.hpp>
  11 : #include <boost/integer/integer_log2.hpp>
  12 : // Code generated by Stan version 2.21.0
  13 : 
  14 : #include <stan/model/model_header.hpp>
  15 : 
  16 : namespace model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1_namespace {
  17 : 
  18 : using std::istream;
  19 : using std::string;
  20 : using std::stringstream;
  21 : using std::vector;
  22 : using stan::io::dump;
  23 : using stan::math::lgamma;
  24 : using stan::model::prob_grad;
  25 : using namespace stan::math;
  26 : 
  27 : static int current_statement_begin__;
  28 : 
  29 : stan::io::program_reader prog_reader__() {
  30 :     stan::io::program_reader reader;
  31 :     reader.add_event(0, 0, "start", "model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1");
  32 :     reader.add_event(3, 1, "end", "model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1");
  33 :     return reader;
  34 : }
  35 : 
  36 : class model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1
  37 :   : public stan::model::model_base_crtp<model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1> {
  38 : private:
  39 :         double y_mean;
  40 : public:
  41 :     model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1(rstan::io::rlist_ref_var_context& context__,
  42 :         std::ostream* pstream__ = 0)
  43 :         : model_base_crtp(0) {
  44 :         ctor_body(context__, 0, pstream__);
  45 :     }
  46 : 
  47 :     model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1(stan::io::var_context& context__,
  48 :         unsigned int random_seed__,
  49 :         std::ostream* pstream__ = 0)
  50 :         : model_base_crtp(0) {
  51 :         ctor_body(context__, random_seed__, pstream__);
  52 :     }
  53 : 
  54 :     void ctor_body(stan::io::var_context& context__,
  55 :                    unsigned int random_seed__,
  56 :                    std::ostream* pstream__) {
  57 :         typedef double local_scalar_t__;
  58 : 
  59 :         boost::ecuyer1988 base_rng__ =
  60 :           stan::services::util::create_rng(random_seed__, 0);
  61 :         (void) base_rng__;  // suppress unused var warning
  62 : 
  63 :         current_statement_begin__ = -1;
  64 : 
  65 :         static const char* function__ = "model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1_namespace::model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1";
  66 :         (void) function__;  // dummy to suppress unused var warning
  67 :         size_t pos__;
  68 :         (void) pos__;  // dummy to suppress unused var warning
  69 :         std::vector<int> vals_i__;
  70 :         std::vector<double> vals_r__;
  71 :         local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
  72 :         (void) DUMMY_VAR__;  // suppress unused var warning
  73 : 
  74 :         try {
  75 :             // initialize data block variables from context__
  76 :             current_statement_begin__ = 1;
  77 :             context__.validate_dims("data initialization", "y_mean", "double", context__.to_vec());
  78 :             y_mean = double(0);
  79 :             vals_r__ = context__.vals_r("y_mean");
  80 :             pos__ = 0;
  81 :             y_mean = vals_r__[pos__++];
  82 : 
  83 : 
  84 :             // initialize transformed data variables
  85 :             // execute transformed data statements
  86 : 
  87 :             // validate transformed data
  88 : 
  89 :             // validate, set parameter ranges
  90 :             num_params_r__ = 0U;
  91 :             param_ranges_i__.clear();
  92 :             current_statement_begin__ = 1;
  93 :             num_params_r__ += 1;
  94 :         } catch (const std::exception& e) {
  95 :             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
  96 :             // Next line prevents compiler griping about no return
  97 :             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
  98 :         }
  99 :     }
 100 : 
 101 :     ~model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1() { }
 102 : 
 103 : 
 104 :     void transform_inits(const stan::io::var_context& context__,
 105 :                          std::vector<int>& params_i__,
 106 :                          std::vector<double>& params_r__,
 107 :                          std::ostream* pstream__) const {
 108 :         typedef double local_scalar_t__;
 109 :         stan::io::writer<double> writer__(params_r__, params_i__);
 110 :         size_t pos__;
 111 :         (void) pos__; // dummy call to supress warning
 112 :         std::vector<double> vals_r__;
 113 :         std::vector<int> vals_i__;
 114 : 
 115 :         current_statement_begin__ = 1;
 116 :         if (!(context__.contains_r("y")))
 117 :             stan::lang::rethrow_located(std::runtime_error(std::string("Variable y missing")), current_statement_begin__, prog_reader__());
 118 :         vals_r__ = context__.vals_r("y");
 119 :         pos__ = 0U;
 120 :         context__.validate_dims("parameter initialization", "y", "double", context__.to_vec());
 121 :         double y(0);
 122 :         y = vals_r__[pos__++];
 123 :         try {
 124 :             writer__.scalar_unconstrain(y);
 125 :         } catch (const std::exception& e) {
 126 :             stan::lang::rethrow_located(std::runtime_error(std::string("Error transforming variable y: ") + e.what()), current_statement_begin__, prog_reader__());
 127 :         }
 128 : 
 129 :         params_r__ = writer__.data_r();
 130 :         params_i__ = writer__.data_i();
 131 :     }
 132 : 
 133 :     void transform_inits(const stan::io::var_context& context,
 134 :                          Eigen::Matrix<double, Eigen::Dynamic, 1>& params_r,
 135 :                          std::ostream* pstream__) const {
 136 :       std::vector<double> params_r_vec;
 137 :       std::vector<int> params_i_vec;
 138 :       transform_inits(context, params_i_vec, params_r_vec, pstream__);
 139 :       params_r.resize(params_r_vec.size());
 140 :       for (int i = 0; i < params_r.size(); ++i)
 141 :         params_r(i) = params_r_vec[i];
 142 :     }
 143 : 
 144 : 
 145 :     template <bool propto__, bool jacobian__, typename T__>
 146 :     T__ log_prob(std::vector<T__>& params_r__,
 147 :                  std::vector<int>& params_i__,
 148 :                  std::ostream* pstream__ = 0) const {
 149 : 
 150 :         typedef T__ local_scalar_t__;
 151 : 
 152 :         local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
 153 :         (void) DUMMY_VAR__;  // dummy to suppress unused var warning
 154 : 
 155 :         T__ lp__(0.0);
 156 :         stan::math::accumulator<T__> lp_accum__;
 157 :         try {
 158 :             stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
 159 : 
 160 :             // model parameters
 161 :             current_statement_begin__ = 1;
 162 :             local_scalar_t__ y;
 163 :             (void) y;  // dummy to suppress unused var warning
 164 :             if (jacobian__)
 165 :                 y = in__.scalar_constrain(lp__);
 166 :             else
 167 :                 y = in__.scalar_constrain();
 168 : 
 169 :             // model body
 170 : 
 171 :             current_statement_begin__ = 1;
 172 :             lp_accum__.add(normal_log<propto__>(y, y_mean, 1));
 173 : 
 174 :         } catch (const std::exception& e) {
 175 :             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
 176 :             // Next line prevents compiler griping about no return
 177 :             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
 178 :         }
 179 : 
 180 :         lp_accum__.add(lp__);
 181 :         return lp_accum__.sum();
 182 : 
 183 :     } // log_prob()
 184 : 
 185 :     template <bool propto, bool jacobian, typename T_>
 186 :     T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
 187 :                std::ostream* pstream = 0) const {
 188 :       std::vector<T_> vec_params_r;
 189 :       vec_params_r.reserve(params_r.size());
 190 :       for (int i = 0; i < params_r.size(); ++i)
 191 :         vec_params_r.push_back(params_r(i));
 192 :       std::vector<int> vec_params_i;
 193 :       return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
 194 :     }
 195 : 
 196 : 
 197 :     void get_param_names(std::vector<std::string>& names__) const {
 198 :         names__.resize(0);
 199 :         names__.push_back("y");
 200 :     }
 201 : 
 202 : 
 203 :     void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
 204 :         dimss__.resize(0);
 205 :         std::vector<size_t> dims__;
 206 :         dims__.resize(0);
 207 :         dimss__.push_back(dims__);
 208 :     }
 209 : 
 210 :     template <typename RNG>
 211 :     void write_array(RNG& base_rng__,
 212 :                      std::vector<double>& params_r__,
 213 :                      std::vector<int>& params_i__,
 214 :                      std::vector<double>& vars__,
 215 :                      bool include_tparams__ = true,
 216 :                      bool include_gqs__ = true,
 217 :                      std::ostream* pstream__ = 0) const {
 218 :         typedef double local_scalar_t__;
 219 : 
 220 :         vars__.resize(0);
 221 :         stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
 222 :         static const char* function__ = "model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1_namespace::write_array";
 223 :         (void) function__;  // dummy to suppress unused var warning
 224 : 
 225 :         // read-transform, write parameters
 226 :         double y = in__.scalar_constrain();
 227 :         vars__.push_back(y);
 228 : 
 229 :         double lp__ = 0.0;
 230 :         (void) lp__;  // dummy to suppress unused var warning
 231 :         stan::math::accumulator<double> lp_accum__;
 232 : 
 233 :         local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
 234 :         (void) DUMMY_VAR__;  // suppress unused var warning
 235 : 
 236 :         if (!include_tparams__ && !include_gqs__) return;
 237 : 
 238 :         try {
 239 :             if (!include_gqs__ && !include_tparams__) return;
 240 :             if (!include_gqs__) return;
 241 :         } catch (const std::exception& e) {
 242 :             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
 243 :             // Next line prevents compiler griping about no return
 244 :             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
 245 :         }
 246 :     }
 247 : 
 248 :     template <typename RNG>
 249 :     void write_array(RNG& base_rng,
 250 :                      Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
 251 :                      Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
 252 :                      bool include_tparams = true,
 253 :                      bool include_gqs = true,
 254 :                      std::ostream* pstream = 0) const {
 255 :       std::vector<double> params_r_vec(params_r.size());
 256 :       for (int i = 0; i < params_r.size(); ++i)
 257 :         params_r_vec[i] = params_r(i);
 258 :       std::vector<double> vars_vec;
 259 :       std::vector<int> params_i_vec;
 260 :       write_array(base_rng, params_r_vec, params_i_vec, vars_vec, include_tparams, include_gqs, pstream);
 261 :       vars.resize(vars_vec.size());
 262 :       for (int i = 0; i < vars.size(); ++i)
 263 :         vars(i) = vars_vec[i];
 264 :     }
 265 : 
 266 :     std::string model_name() const {
 267 :         return "model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1";
 268 :     }
 269 : 
 270 : 
 271 :     void constrained_param_names(std::vector<std::string>& param_names__,
 272 :                                  bool include_tparams__ = true,
 273 :                                  bool include_gqs__ = true) const {
 274 :         std::stringstream param_name_stream__;
 275 :         param_name_stream__.str(std::string());
 276 :         param_name_stream__ << "y";
 277 :         param_names__.push_back(param_name_stream__.str());
 278 : 
 279 :         if (!include_gqs__ && !include_tparams__) return;
 280 : 
 281 :         if (include_tparams__) {
 282 :         }
 283 : 
 284 :         if (!include_gqs__) return;
 285 :     }
 286 : 
 287 : 
 288 :     void unconstrained_param_names(std::vector<std::string>& param_names__,
 289 :                                    bool include_tparams__ = true,
 290 :                                    bool include_gqs__ = true) const {
 291 :         std::stringstream param_name_stream__;
 292 :         param_name_stream__.str(std::string());
 293 :         param_name_stream__ << "y";
 294 :         param_names__.push_back(param_name_stream__.str());
 295 : 
 296 :         if (!include_gqs__ && !include_tparams__) return;
 297 : 
 298 :         if (include_tparams__) {
 299 :         }
 300 : 
 301 :         if (!include_gqs__) return;
 302 :     }
 303 : 
 304 : }; // model
 305 : 
 306 : }  // namespace
 307 : 
 308 : typedef model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1_namespace::model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1 stan_model;
 309 : 
 310 : #ifndef USING_R
 311 : 
 312 : stan::model::model_base& new_model(
 313 :         stan::io::var_context& data_context,
 314 :         unsigned int seed,
 315 :         std::ostream* msg_stream) {
 316 :   stan_model* m = new stan_model(data_context, seed, msg_stream);
 317 :   return *m;
 318 : }
 319 : 
 320 : #endif
 321 : 
 322 : 
 323 : 
 324 : #include <rstan_next/stan_fit.hpp>
 325 : 
 326 : struct stan_model_holder {
 327 :     stan_model_holder(rstan::io::rlist_ref_var_context rcontext,
 328 :                       unsigned int random_seed)
 329 :     : rcontext_(rcontext), random_seed_(random_seed)
 330 :      {
 331 :      }
 332 : 
 333 :    //stan::math::ChainableStack ad_stack;
 334 :    rstan::io::rlist_ref_var_context rcontext_;
 335 :    unsigned int random_seed_;
 336 : };
 337 : 
 338 : Rcpp::XPtr<stan::model::model_base> model_ptr(stan_model_holder* smh) {
 339 :   Rcpp::XPtr<stan::model::model_base> model_instance(new stan_model(smh->rcontext_, smh->random_seed_), true);
 340 :   return model_instance;
 341 : }
 342 : 
 343 : Rcpp::XPtr<rstan::stan_fit_base> fit_ptr(stan_model_holder* smh) {
 344 :   return Rcpp::XPtr<rstan::stan_fit_base>(new rstan::stan_fit(model_ptr(smh), smh->random_seed_), true);
 345 : }
 346 : 
 347 : std::string model_name(stan_model_holder* smh) {
 348 :   return model_ptr(smh).get()->model_name();
 349 : }
 350 : 
 351 : RCPP_MODULE(stan_fit4model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1_mod){
 352 :   Rcpp::class_<stan_model_holder>("stan_fit4model285c797b24a8_73fc79f8b1915e8208c736914c86d1a1")
 353 :   .constructor<rstan::io::rlist_ref_var_context, unsigned int>()
 354 :   .method("model_ptr", &model_ptr)
 355 :   .method("fit_ptr", &fit_ptr)
 356 :   .method("model_name", &model_name)
 357 :   ;
 358 : }
 359 : 
 360 : 
 361 : // declarations
 362 : extern "C" {
 363 : SEXP file285c2e2b7aba( ) ;
 364 : }
 365 : 
 366 : // definition
 367 : 
 368 : SEXP file285c2e2b7aba(  ){
 369 :  return Rcpp::wrap("73fc79f8b1915e8208c736914c86d1a1");
 370 : }
 371 : 
 372 : 
Compilation argument:
 C:/PROGRA~1/R/R-40~1.2/bin/x64/R CMD SHLIB file285c2e2b7aba.cpp 2> file285c2e2b7aba.cpp.err.txt 
"C:/rtools40/mingw64/bin/"g++  -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG   -I"C:/Program Files/R/R-4.0.2/library/Rcpp/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppEigen/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppEigen/include/unsupported"  -I"C:/Program Files/R/R-4.0.2/library/BH/include" -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src/"  -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/"  -I"C:/Program Files/R/R-4.0.2/library/RcppParallel/include/"  -I"C:/Program Files/R/R-4.0.2/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include "C:/Program Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp"  -std=c++1y    -march=corei7   -include C:/Program Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I "C:/Program Files/R/R-4.0.2/library/StanHeaders/include" -I "C:/Program Files/R/R-4.0.2/library/RcppEigen/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file285c2e2b7aba.cpp -o file285c2e2b7aba.o
g++.exe: error: Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file285c2e2b7aba.o] Error 1
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
2: In file(con, "r") :
  cannot open file 'file285c2e2b7aba.cpp.err.txt': No such file or directory

Actually this:

g++.exe: error: Files/R/R-4.0.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory

vs.

-I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src/"

Is it the space in “Program Files” that is causing problems? @andrjohns have you seen this before? I don’t know if this is actually the problem, but I’d be inclined to try putting your R library in another folder (one without spaces).

1 Like

Yep, that looks like what was happening over in this post, where using rstan::stan() instead of loading RStan was a workaround.

I thought @bgoodri fixed it in RStan 2.21 though, so this might be new

2 Likes

That is funny at how easy a fix this was and not funny at how long it took. The model samples and finishes but I do get this warning message

Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found

Adding in what I did:
Moved R from Program Files up one directory so it is now in C:\R

3 Likes

I think the fix for that warning is to add:

CXX = C:/rtools40/usr/mingw$WIN/bin/g++

To your Makevars.win file

Same warning message
Makevars.win

CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
CXX14 = C:/rtools40/usr/mingw$WIN/bin/g++

Oh sorry, two errors here. There shouldn’t be a /usr/ folder in that address and there should be an added line for CXX:

CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
CXX14 = C:/rtools40/mingw$WIN/bin/g++
CXX = C:/rtools40/mingw$WIN/bin/g++

I’m glad you guys are so patient :p (and thank you for all your help + @bbbales2, @rok_cesnovar)

I added the lines and completely closed out of Rstudio to get a clean session, however, same warning

CXX14FLAGS=-O3 -mtune=native -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
CXX14 = C:/rtools40/mingw$WIN/bin/g++
CXX = C:/rtools40/mingw$WIN/bin/g++

Can you try running

Sys.setenv(CXX = "C:/rtools40/mingw$(WIN)/bin/g++")
Sys.setenv(CXX14 = "C:/rtools40/mingw$(WIN)/bin/g++")

And then running your model?

Just edited the commands to fix a missing slash

Still getting that warning :(. I restarted rstudio just to make sure too.

What do you get from Sys.getenv("CXX")?

“” – basically nothing

Hmm will have to troubleshoot locally tomorrow when I get to a windows machine, will have to get back to you sorry!

1 Like