RStan 2.10 error

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Mikes-MacBook-Air:~ mike$ R

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
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Platform: x86_64-apple-darwin13.4.0 (64-bit)

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> setwd("~/_/Programming/bayes_days/01_one_group1")
> model = rstan::stan_model(file='01_one_group1.stan')
In file included from file404625e1dd5.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:232:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr.hpp:33:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:81:37: error: no member named 'max_step_checker' in namespace 'boost::numeric::odeint'
      using boost::numeric::odeint::max_step_checker;
            ~~~~~~~~~~~~~~~~~~~~~~~~^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:136:23: error: use of undeclared identifier 'max_step_checker'
                      max_step_checker(max_num_steps));
                      ^
2 errors generated.
make: *** [file404625e1dd5.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 2.10
  7: 
  8: #include <stan/model/model_header.hpp>
  9: 
 10: namespace model4046f818d37_01_one_group1_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: class model4046f818d37_01_one_group1 : public prob_grad {
 28: private:
 29:     int nY;
 30:     vector_d Y;
 31: public:
 32:     model4046f818d37_01_one_group1(stan::io::var_context& context__,
 33:         std::ostream* pstream__ = 0)
 34:         : prob_grad(0) {
 35:         current_statement_begin__ = -1;
 36: 
 37:         static const char* function__ = "model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1";
 38:         (void) function__; // dummy call to supress warning
 39:         size_t pos__;
 40:         (void) pos__; // dummy call to supress warning
 41:         std::vector<int> vals_i__;
 42:         std::vector<double> vals_r__;
 43:         context__.validate_dims("data initialization", "nY", "int", context__.to_vec());
 44:         nY = int(0);
 45:         vals_i__ = context__.vals_i("nY");
 46:         pos__ = 0;
 47:         nY = vals_i__[pos__++];
 48:         validate_non_negative_index("Y", "nY", nY);
 49:         Y = vector_d(static_cast<Eigen::VectorXd::Index>(nY));
 50:         context__.validate_dims("data initialization", "Y", "vector_d", context__.to_vec(nY));
 51:         vals_r__ = context__.vals_r("Y");
 52:         pos__ = 0;
 53:         size_t Y_i_vec_lim__ = nY;
 54:         for (size_t i_vec__ = 0; i_vec__ < Y_i_vec_lim__; ++i_vec__) {
 55:             Y[i_vec__] = vals_r__[pos__++];
 56:         }
 57: 
 58:         // validate data
 59: 
 60:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
 61:         (void) DUMMY_VAR__;  // suppress unused var warning
 62: 
 63: 
 64:         // initialize transformed variables to avoid seg fault on val access
 65: 
 66:         try {
 67:         } catch (const std::exception& e) {
 68:             stan::lang::rethrow_located(e,current_statement_begin__);
 69:             // Next line prevents compiler griping about no return
 70:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
 71:         }
 72: 
 73:         // validate transformed data
 74: 
 75:         // set parameter ranges
 76:         num_params_r__ = 0U;
 77:         param_ranges_i__.clear();
 78:         ++num_params_r__;
 79:     }
 80: 
 81:     ~model4046f818d37_01_one_group1() { }
 82: 
 83: 
 84:     void transform_inits(const stan::io::var_context& context__,
 85:                          std::vector<int>& params_i__,
 86:                          std::vector<double>& params_r__,
 87:                          std::ostream* pstream__) const {
 88:         stan::io::writer<double> writer__(params_r__,params_i__);
 89:         size_t pos__;
 90:         (void) pos__; // dummy call to supress warning
 91:         std::vector<double> vals_r__;
 92:         std::vector<int> vals_i__;
 93: 
 94:         if (!(context__.contains_r("mu")))
 95:             throw std::runtime_error("variable mu missing");
 96:         vals_r__ = context__.vals_r("mu");
 97:         pos__ = 0U;
 98:         context__.validate_dims("initialization", "mu", "double", context__.to_vec());
 99:         double mu(0);
100:         mu = vals_r__[pos__++];
101:         try {
102:             writer__.scalar_unconstrain(mu);
103:         } catch (const std::exception& e) { 
104:             throw std::runtime_error(std::string("Error transforming variable mu: ") + e.what());
105:         }
106: 
107:         params_r__ = writer__.data_r();
108:         params_i__ = writer__.data_i();
109:     }
110: 
111:     void transform_inits(const stan::io::var_context& context,
112:                          Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
113:                          std::ostream* pstream__) const {
114:       std::vector<double> params_r_vec;
115:       std::vector<int> params_i_vec;
116:       transform_inits(context, params_i_vec, params_r_vec, pstream__);
117:       params_r.resize(params_r_vec.size());
118:       for (int i = 0; i < params_r.size(); ++i)
119:         params_r(i) = params_r_vec[i];
120:     }
121: 
122: 
123:     template <bool propto__, bool jacobian__, typename T__>
124:     T__ log_prob(vector<T__>& params_r__,
125:                  vector<int>& params_i__,
126:                  std::ostream* pstream__ = 0) const {
127: 
128:         T__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
129:         (void) DUMMY_VAR__;  // suppress unused var warning
130: 
131:         T__ lp__(0.0);
132:         stan::math::accumulator<T__> lp_accum__;
133: 
134:         // model parameters
135:         stan::io::reader<T__> in__(params_r__,params_i__);
136: 
137:         T__ mu;
138:         (void) mu;  // dummy to suppress unused var warning
139:         if (jacobian__)
140:             mu = in__.scalar_constrain(lp__);
141:         else
142:             mu = in__.scalar_constrain();
143: 
144: 
145:         // transformed parameters
146: 
147:         // initialize transformed variables to avoid seg fault on val access
148: 
149:         try {
150:         } catch (const std::exception& e) {
151:             stan::lang::rethrow_located(e,current_statement_begin__);
152:             // Next line prevents compiler griping about no return
153:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
154:         }
155: 
156:         // validate transformed parameters
157: 
158:         const char* function__ = "validate transformed params";
159:         (void) function__;  // dummy to suppress unused var warning
160: 
161:         // model body
162:         try {
163:             current_statement_begin__ = 10;
164:             lp_accum__.add(normal_log<propto__>(mu, 100, 20));
165:             current_statement_begin__ = 11;
166:             lp_accum__.add(normal_log<propto__>(Y, mu, 15));
167:         } catch (const std::exception& e) {
168:             stan::lang::rethrow_located(e,current_statement_begin__);
169:             // Next line prevents compiler griping about no return
170:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
171:         }
172: 
173:         lp_accum__.add(lp__);
174:         return lp_accum__.sum();
175: 
176:     } // log_prob()
177: 
178:     template <bool propto, bool jacobian, typename T_>
179:     T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
180:                std::ostream* pstream = 0) const {
181:       std::vector<T_> vec_params_r;
182:       vec_params_r.reserve(params_r.size());
183:       for (int i = 0; i < params_r.size(); ++i)
184:         vec_params_r.push_back(params_r(i));
185:       std::vector<int> vec_params_i;
186:       return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
187:     }
188: 
189: 
190:     void get_param_names(std::vector<std::string>& names__) const {
191:         names__.resize(0);
192:         names__.push_back("mu");
193:     }
194: 
195: 
196:     void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
197:         dimss__.resize(0);
198:         std::vector<size_t> dims__;
199:         dims__.resize(0);
200:         dimss__.push_back(dims__);
201:     }
202: 
203:     template <typename RNG>
204:     void write_array(RNG& base_rng__,
205:                      std::vector<double>& params_r__,
206:                      std::vector<int>& params_i__,
207:                      std::vector<double>& vars__,
208:                      bool include_tparams__ = true,
209:                      bool include_gqs__ = true,
210:                      std::ostream* pstream__ = 0) const {
211:         vars__.resize(0);
212:         stan::io::reader<double> in__(params_r__,params_i__);
213:         static const char* function__ = "model4046f818d37_01_one_group1_namespace::write_array";
214:         (void) function__; // dummy call to supress warning
215:         // read-transform, write parameters
216:         double mu = in__.scalar_constrain();
217:         vars__.push_back(mu);
218: 
219:         if (!include_tparams__) return;
220:         // declare and define transformed parameters
221:         double lp__ = 0.0;
222:         (void) lp__; // dummy call to supress warning
223:         stan::math::accumulator<double> lp_accum__;
224: 
225: 
226:         try {
227:         } catch (const std::exception& e) {
228:             stan::lang::rethrow_located(e,current_statement_begin__);
229:             // Next line prevents compiler griping about no return
230:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
231:         }
232: 
233:         // validate transformed parameters
234: 
235:         // write transformed parameters
236: 
237:         if (!include_gqs__) return;
238:         // declare and define generated quantities
239: 
240:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
241:         (void) DUMMY_VAR__;  // suppress unused var warning
242: 
243: 
244:         // initialize transformed variables to avoid seg fault on val access
245: 
246:         try {
247:         } catch (const std::exception& e) {
248:             stan::lang::rethrow_located(e,current_statement_begin__);
249:             // Next line prevents compiler griping about no return
250:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
251:         }
252: 
253:         // validate generated quantities
254: 
255:         // write generated quantities
256:     }
257: 
258:     template <typename RNG>
259:     void write_array(RNG& base_rng,
260:                      Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
261:                      Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
262:                      bool include_tparams = true,
263:                      bool include_gqs = true,
264:                      std::ostream* pstream = 0) const {
265:       std::vector<double> params_r_vec(params_r.size());
266:       for (int i = 0; i < params_r.size(); ++i)
267:         params_r_vec[i] = params_r(i);
268:       std::vector<double> vars_vec;
269:       std::vector<int> params_i_vec;
270:       write_array(base_rng,params_r_vec,params_i_vec,vars_vec,include_tparams,include_gqs,pstream);
271:       vars.resize(vars_vec.size());
272:       for (int i = 0; i < vars.size(); ++i)
273:         vars(i) = vars_vec[i];
274:     }
275: 
276:     static std::string model_name() {
277:         return "model4046f818d37_01_one_group1";
278:     }
279: 
280: 
281:     void constrained_param_names(std::vector<std::string>& param_names__,
282:                                  bool include_tparams__ = true,
283:                                  bool include_gqs__ = true) const {
284:         std::stringstream param_name_stream__;
285:         param_name_stream__.str(std::string());
286:         param_name_stream__ << "mu";
287:         param_names__.push_back(param_name_stream__.str());
288: 
289:         if (!include_gqs__ && !include_tparams__) return;
290: 
291:         if (!include_gqs__) return;
292:     }
293: 
294: 
295:     void unconstrained_param_names(std::vector<std::string>& param_names__,
296:                                    bool include_tparams__ = true,
297:                                    bool include_gqs__ = true) const {
298:         std::stringstream param_name_stream__;
299:         param_name_stream__.str(std::string());
300:         param_name_stream__ << "mu";
301:         param_names__.push_back(param_name_stream__.str());
302: 
303:         if (!include_gqs__ && !include_tparams__) return;
304: 
305:         if (!include_gqs__) return;
306:     }
307: 
308: }; // model
309: 
310: } // namespace
311: 
312: typedef model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1 stan_model;
313: 
314: #include <rstan/rstaninc.hpp>
315: /**
316:  * Define Rcpp Module to expose stan_fit's functions to R.
317:  */
318: RCPP_MODULE(stan_fit4model4046f818d37_01_one_group1_mod){
319:   Rcpp::class_<rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1,
320:                boost::random::ecuyer1988> >("stan_fit4model4046f818d37_01_one_group1")
321:     // .constructor<Rcpp::List>()
322:     .constructor<SEXP, SEXP>()
323:     // .constructor<SEXP, SEXP>()
324:     .method("call_sampler",
325:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::call_sampler)
326:     .method("param_names",
327:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::param_names)
328:     .method("param_names_oi",
329:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::param_names_oi)
330:     .method("param_fnames_oi",
331:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::param_fnames_oi)
332:     .method("param_dims",
333:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::param_dims)
334:     .method("param_dims_oi",
335:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::param_dims_oi)
336:     .method("update_param_oi",
337:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::update_param_oi)
338:     .method("param_oi_tidx",
339:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::param_oi_tidx)
340:     .method("grad_log_prob",
341:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::grad_log_prob)
342:     .method("log_prob",
343:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::log_prob)
344:     .method("unconstrain_pars",
345:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::unconstrain_pars)
346:     .method("constrain_pars",
347:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::constrain_pars)
348:     .method("num_pars_unconstrained",
349:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::num_pars_unconstrained)
350:     .method("unconstrained_param_names",
351:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::unconstrained_param_names)
352:     .method("constrained_param_names",
353:             &rstan::stan_fit<model4046f818d37_01_one_group1_namespace::model4046f818d37_01_one_group1, boost::random::ecuyer1988>::constrained_param_names)
354:     ;
355: }
356: 
357: // declarations
358: extern "C" {
359: SEXP file404625e1dd5( ) ;
360: }
361: 
362: // definition
363: 
364: SEXP file404625e1dd5(  ){
365:  return Rcpp::wrap("01_one_group1");
366: }
367: 
368: 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from file404625e1dd5.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:232:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr.hpp:33:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:81:37: error: no member named 'max_step_checker' in namespace 'boost::numeric::odeint'
      using bo
In addition: Warning message:
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file404625e1dd5.cpp 2> file404625e1dd5.cpp.err.txt' had status 1 
>