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LauritsDixen/new example(stan_model, package = "rstan", run.dontrun = TRUE)

Created November 8, 2019 06:54
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results from "example(stan_model, package = "rstan", run.dontrun = TRUE)" with "-Wno-ignored-attributes" at CXX14FLAGS
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new example(stan_model, package = "rstan", run.dontrun = TRUE)
TRANSLATING MODEL '16a540c6086086816528e4524def24d9' FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model '16a540c6086086816528e4524def24d9'.
COMPILING THE C++ CODE FOR MODEL '16a540c6086086816528e4524def24d9' NOW.
OS: x86_64, linux-gnu; rstan: 2.19.2; Rcpp: 1.0.2; inline: 0.3.15
>> setting environment variables:
PKG_LIBS = -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders
PKG_CPPFLAGS = -I"/usr/local/lib/R/site-library/Rcpp/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/" -I"/usr/local/lib/R/site-library/StanHeaders/include/" -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS
>> Program source :
1 :
2 : // includes from the plugin
3 : // [[Rcpp::plugins(cpp14)]]
4 :
5 : // user includes
6 : #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.19.1
7 :
8 : #include <stan/model/model_header.hpp>
9 :
10 : namespace model23d979577990_16a540c6086086816528e4524def24d9_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 : static int current_statement_begin__;
22 :
23 : stan::io::program_reader prog_reader__() {
24 : stan::io::program_reader reader;
25 : reader.add_event(0, 0, "start", "model23d979577990_16a540c6086086816528e4524def24d9");
26 : reader.add_event(3, 1, "end", "model23d979577990_16a540c6086086816528e4524def24d9");
27 : return reader;
28 : }
29 :
30 : class model23d979577990_16a540c6086086816528e4524def24d9 : public prob_grad {
31 : private:
32 : double y_mean;
33 : public:
34 : model23d979577990_16a540c6086086816528e4524def24d9(stan::io::var_context& context__,
35 : std::ostream* pstream__ = 0)
36 : : prob_grad(0) {
37 : ctor_body(context__, 0, pstream__);
38 : }
39 :
40 : model23d979577990_16a540c6086086816528e4524def24d9(stan::io::var_context& context__,
41 : unsigned int random_seed__,
42 : std::ostream* pstream__ = 0)
43 : : prob_grad(0) {
44 : ctor_body(context__, random_seed__, pstream__);
45 : }
46 :
47 : void ctor_body(stan::io::var_context& context__,
48 : unsigned int random_seed__,
49 : std::ostream* pstream__) {
50 : typedef double local_scalar_t__;
51 :
52 : boost::ecuyer1988 base_rng__ =
53 : stan::services::util::create_rng(random_seed__, 0);
54 : (void) base_rng__; // suppress unused var warning
55 :
56 : current_statement_begin__ = -1;
57 :
58 : static const char* function__ = "model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9";
59 : (void) function__; // dummy to suppress unused var warning
60 : size_t pos__;
61 : (void) pos__; // dummy to suppress unused var warning
62 : std::vector<int> vals_i__;
63 : std::vector<double> vals_r__;
64 : local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
65 : (void) DUMMY_VAR__; // suppress unused var warning
66 :
67 : try {
68 : // initialize data block variables from context__
69 : current_statement_begin__ = 1;
70 : context__.validate_dims("data initialization", "y_mean", "double", context__.to_vec());
71 : y_mean = double(0);
72 : vals_r__ = context__.vals_r("y_mean");
73 : pos__ = 0;
74 : y_mean = vals_r__[pos__++];
75 :
76 :
77 : // initialize transformed data variables
78 : // execute transformed data statements
79 :
80 : // validate transformed data
81 :
82 : // validate, set parameter ranges
83 : num_params_r__ = 0U;
84 : param_ranges_i__.clear();
85 : current_statement_begin__ = 1;
86 : num_params_r__ += 1;
87 : } catch (const std::exception& e) {
88 : stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
89 : // Next line prevents compiler griping about no return
90 : throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
91 : }
92 : }
93 :
94 : ~model23d979577990_16a540c6086086816528e4524def24d9() { }
95 :
96 :
97 : void transform_inits(const stan::io::var_context& context__,
98 : std::vector<int>& params_i__,
99 : std::vector<double>& params_r__,
100 : std::ostream* pstream__) const {
101 : typedef double local_scalar_t__;
102 : stan::io::writer<double> writer__(params_r__, params_i__);
103 : size_t pos__;
104 : (void) pos__; // dummy call to supress warning
105 : std::vector<double> vals_r__;
106 : std::vector<int> vals_i__;
107 :
108 : current_statement_begin__ = 1;
109 : if (!(context__.contains_r("y")))
110 : stan::lang::rethrow_located(std::runtime_error(std::string("Variable y missing")), current_statement_begin__, prog_reader__());
111 : vals_r__ = context__.vals_r("y");
112 : pos__ = 0U;
113 : context__.validate_dims("parameter initialization", "y", "double", context__.to_vec());
114 : double y(0);
115 : y = vals_r__[pos__++];
116 : try {
117 : writer__.scalar_unconstrain(y);
118 : } catch (const std::exception& e) {
119 : stan::lang::rethrow_located(std::runtime_error(std::string("Error transforming variable y: ") + e.what()), current_statement_begin__, prog_reader__());
120 : }
121 :
122 : params_r__ = writer__.data_r();
123 : params_i__ = writer__.data_i();
124 : }
125 :
126 : void transform_inits(const stan::io::var_context& context,
127 : Eigen::Matrix<double, Eigen::Dynamic, 1>& params_r,
128 : std::ostream* pstream__) const {
129 : std::vector<double> params_r_vec;
130 : std::vector<int> params_i_vec;
131 : transform_inits(context, params_i_vec, params_r_vec, pstream__);
132 : params_r.resize(params_r_vec.size());
133 : for (int i = 0; i < params_r.size(); ++i)
134 : params_r(i) = params_r_vec[i];
135 : }
136 :
137 :
138 : template <bool propto__, bool jacobian__, typename T__>
139 : T__ log_prob(std::vector<T__>& params_r__,
140 : std::vector<int>& params_i__,
141 : std::ostream* pstream__ = 0) const {
142 :
143 : typedef T__ local_scalar_t__;
144 :
145 : local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
146 : (void) DUMMY_VAR__; // dummy to suppress unused var warning
147 :
148 : T__ lp__(0.0);
149 : stan::math::accumulator<T__> lp_accum__;
150 : try {
151 : stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
152 :
153 : // model parameters
154 : current_statement_begin__ = 1;
155 : local_scalar_t__ y;
156 : (void) y; // dummy to suppress unused var warning
157 : if (jacobian__)
158 : y = in__.scalar_constrain(lp__);
159 : else
160 : y = in__.scalar_constrain();
161 :
162 : // model body
163 :
164 : current_statement_begin__ = 1;
165 : lp_accum__.add(normal_log<propto__>(y, y_mean, 1));
166 :
167 : } catch (const std::exception& e) {
168 : stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
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("y");
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 : typedef double local_scalar_t__;
212 :
213 : vars__.resize(0);
214 : stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
215 : static const char* function__ = "model23d979577990_16a540c6086086816528e4524def24d9_namespace::write_array";
216 : (void) function__; // dummy to suppress unused var warning
217 :
218 : // read-transform, write parameters
219 : double y = in__.scalar_constrain();
220 : vars__.push_back(y);
221 :
222 : double lp__ = 0.0;
223 : (void) lp__; // dummy to suppress unused var warning
224 : stan::math::accumulator<double> lp_accum__;
225 :
226 : local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
227 : (void) DUMMY_VAR__; // suppress unused var warning
228 :
229 : if (!include_tparams__ && !include_gqs__) return;
230 :
231 : try {
232 : if (!include_gqs__ && !include_tparams__) return;
233 : if (!include_gqs__) return;
234 : } catch (const std::exception& e) {
235 : stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
236 : // Next line prevents compiler griping about no return
237 : throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
238 : }
239 : }
240 :
241 : template <typename RNG>
242 : void write_array(RNG& base_rng,
243 : Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
244 : Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
245 : bool include_tparams = true,
246 : bool include_gqs = true,
247 : std::ostream* pstream = 0) const {
248 : std::vector<double> params_r_vec(params_r.size());
249 : for (int i = 0; i < params_r.size(); ++i)
250 : params_r_vec[i] = params_r(i);
251 : std::vector<double> vars_vec;
252 : std::vector<int> params_i_vec;
253 : write_array(base_rng, params_r_vec, params_i_vec, vars_vec, include_tparams, include_gqs, pstream);
254 : vars.resize(vars_vec.size());
255 : for (int i = 0; i < vars.size(); ++i)
256 : vars(i) = vars_vec[i];
257 : }
258 :
259 : static std::string model_name() {
260 : return "model23d979577990_16a540c6086086816528e4524def24d9";
261 : }
262 :
263 :
264 : void constrained_param_names(std::vector<std::string>& param_names__,
265 : bool include_tparams__ = true,
266 : bool include_gqs__ = true) const {
267 : std::stringstream param_name_stream__;
268 : param_name_stream__.str(std::string());
269 : param_name_stream__ << "y";
270 : param_names__.push_back(param_name_stream__.str());
271 :
272 : if (!include_gqs__ && !include_tparams__) return;
273 :
274 : if (include_tparams__) {
275 : }
276 :
277 : if (!include_gqs__) return;
278 : }
279 :
280 :
281 : void unconstrained_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__ << "y";
287 : param_names__.push_back(param_name_stream__.str());
288 :
289 : if (!include_gqs__ && !include_tparams__) return;
290 :
291 : if (include_tparams__) {
292 : }
293 :
294 : if (!include_gqs__) return;
295 : }
296 :
297 : }; // model
298 :
299 : } // namespace
300 :
301 : typedef model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9 stan_model;
302 :
303 : #include <rstan/rstaninc.hpp>
304 : /**
305 : * Define Rcpp Module to expose stan_fit's functions to R.
306 : */
307 : RCPP_MODULE(stan_fit4model23d979577990_16a540c6086086816528e4524def24d9_mod){
308 : Rcpp::class_<rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9,
309 : boost::random::ecuyer1988> >("stan_fit4model23d979577990_16a540c6086086816528e4524def24d9")
310 : // .constructor<Rcpp::List>()
311 : .constructor<SEXP, SEXP, SEXP>()
312 : // .constructor<SEXP, SEXP>()
313 : .method("call_sampler",
314 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::call_sampler)
315 : .method("param_names",
316 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_names)
317 : .method("param_names_oi",
318 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_names_oi)
319 : .method("param_fnames_oi",
320 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_fnames_oi)
321 : .method("param_dims",
322 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_dims)
323 : .method("param_dims_oi",
324 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_dims_oi)
325 : .method("update_param_oi",
326 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::update_param_oi)
327 : .method("param_oi_tidx",
328 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_oi_tidx)
329 : .method("grad_log_prob",
330 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::grad_log_prob)
331 : .method("log_prob",
332 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::log_prob)
333 : .method("unconstrain_pars",
334 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::unconstrain_pars)
335 : .method("constrain_pars",
336 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::constrain_pars)
337 : .method("num_pars_unconstrained",
338 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::num_pars_unconstrained)
339 : .method("unconstrained_param_names",
340 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::unconstrained_param_names)
341 : .method("constrained_param_names",
342 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::constrained_param_names)
343 : .method("standalone_gqs",
344 : &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::standalone_gqs)
345 : ;
346 : }
347 :
348 : // declarations
349 : extern "C" {
350 : SEXP file23d9659a9ab6( ) ;
351 : }
352 :
353 : // definition
354 :
355 : SEXP file23d9659a9ab6( ){
356 : return Rcpp::wrap("16a540c6086086816528e4524def24d9");
357 : }
358 :
359 :
Compilation argument:
/usr/lib/R/bin/R CMD SHLIB file23d9659a9ab6.cpp 2> file23d9659a9ab6.cpp.err.txt
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/" -I"/usr/local/lib/R/site-library/StanHeaders/include/" -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -fpic -O3 -march=native -mtune=native -fPIC -Wno-ignored-attributes -c file23d9659a9ab6.cpp -o file23d9659a9ab6.o
/usr/lib/R/etc/Makeconf:176: recipe for target 'file23d9659a9ab6.o' failed
In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /usr/local/lib/R/site-library/BH/include/boost/random/detail/int_float_pair.hpp:26,
from /usr/local/lib/R/site-library/BH/include/boost/random/exponential_distribution.hpp:27,
from /usr/local/lib/R/site-library/BH/include/boost/random/gamma_distribution.hpp:25,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:292,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/usr/local/lib/R/site-library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
In file included from /usr/local/lib/R/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
from /usr/local/lib/R/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /usr/local/lib/R/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /usr/local/lib/R/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /usr/local/lib/R/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /usr/local/lib/R/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /usr/local/lib/R/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /usr/local/lib/R/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/arr.hpp:46,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:344,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /usr/local/lib/R/site-library/BH/include/boost/lexical_cast.hpp:32,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /usr/local/lib/R/site-library/BH/include/boost/math/constants/constants.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
make: *** [file23d9659a9ab6.o] Error 4
ERROR(s) during compilation: source code errors or compiler configuration errors!
Program source:
1:
2: // includes from the plugin
3: // [[Rcpp::plugins(cpp14)]]
4:
5: // user includes
6: #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.19.1
7:
8: #include <stan/model/model_header.hpp>
9:
10: namespace model23d979577990_16a540c6086086816528e4524def24d9_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: static int current_statement_begin__;
22:
23: stan::io::program_reader prog_reader__() {
24: stan::io::program_reader reader;
25: reader.add_event(0, 0, "start", "model23d979577990_16a540c6086086816528e4524def24d9");
26: reader.add_event(3, 1, "end", "model23d979577990_16a540c6086086816528e4524def24d9");
27: return reader;
28: }
29:
30: class model23d979577990_16a540c6086086816528e4524def24d9 : public prob_grad {
31: private:
32: double y_mean;
33: public:
34: model23d979577990_16a540c6086086816528e4524def24d9(stan::io::var_context& context__,
35: std::ostream* pstream__ = 0)
36: : prob_grad(0) {
37: ctor_body(context__, 0, pstream__);
38: }
39:
40: model23d979577990_16a540c6086086816528e4524def24d9(stan::io::var_context& context__,
41: unsigned int random_seed__,
42: std::ostream* pstream__ = 0)
43: : prob_grad(0) {
44: ctor_body(context__, random_seed__, pstream__);
45: }
46:
47: void ctor_body(stan::io::var_context& context__,
48: unsigned int random_seed__,
49: std::ostream* pstream__) {
50: typedef double local_scalar_t__;
51:
52: boost::ecuyer1988 base_rng__ =
53: stan::services::util::create_rng(random_seed__, 0);
54: (void) base_rng__; // suppress unused var warning
55:
56: current_statement_begin__ = -1;
57:
58: static const char* function__ = "model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9";
59: (void) function__; // dummy to suppress unused var warning
60: size_t pos__;
61: (void) pos__; // dummy to suppress unused var warning
62: std::vector<int> vals_i__;
63: std::vector<double> vals_r__;
64: local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
65: (void) DUMMY_VAR__; // suppress unused var warning
66:
67: try {
68: // initialize data block variables from context__
69: current_statement_begin__ = 1;
70: context__.validate_dims("data initialization", "y_mean", "double", context__.to_vec());
71: y_mean = double(0);
72: vals_r__ = context__.vals_r("y_mean");
73: pos__ = 0;
74: y_mean = vals_r__[pos__++];
75:
76:
77: // initialize transformed data variables
78: // execute transformed data statements
79:
80: // validate transformed data
81:
82: // validate, set parameter ranges
83: num_params_r__ = 0U;
84: param_ranges_i__.clear();
85: current_statement_begin__ = 1;
86: num_params_r__ += 1;
87: } catch (const std::exception& e) {
88: stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
89: // Next line prevents compiler griping about no return
90: throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
91: }
92: }
93:
94: ~model23d979577990_16a540c6086086816528e4524def24d9() { }
95:
96:
97: void transform_inits(const stan::io::var_context& context__,
98: std::vector<int>& params_i__,
99: std::vector<double>& params_r__,
100: std::ostream* pstream__) const {
101: typedef double local_scalar_t__;
102: stan::io::writer<double> writer__(params_r__, params_i__);
103: size_t pos__;
104: (void) pos__; // dummy call to supress warning
105: std::vector<double> vals_r__;
106: std::vector<int> vals_i__;
107:
108: current_statement_begin__ = 1;
109: if (!(context__.contains_r("y")))
110: stan::lang::rethrow_located(std::runtime_error(std::string("Variable y missing")), current_statement_begin__, prog_reader__());
111: vals_r__ = context__.vals_r("y");
112: pos__ = 0U;
113: context__.validate_dims("parameter initialization", "y", "double", context__.to_vec());
114: double y(0);
115: y = vals_r__[pos__++];
116: try {
117: writer__.scalar_unconstrain(y);
118: } catch (const std::exception& e) {
119: stan::lang::rethrow_located(std::runtime_error(std::string("Error transforming variable y: ") + e.what()), current_statement_begin__, prog_reader__());
120: }
121:
122: params_r__ = writer__.data_r();
123: params_i__ = writer__.data_i();
124: }
125:
126: void transform_inits(const stan::io::var_context& context,
127: Eigen::Matrix<double, Eigen::Dynamic, 1>& params_r,
128: std::ostream* pstream__) const {
129: std::vector<double> params_r_vec;
130: std::vector<int> params_i_vec;
131: transform_inits(context, params_i_vec, params_r_vec, pstream__);
132: params_r.resize(params_r_vec.size());
133: for (int i = 0; i < params_r.size(); ++i)
134: params_r(i) = params_r_vec[i];
135: }
136:
137:
138: template <bool propto__, bool jacobian__, typename T__>
139: T__ log_prob(std::vector<T__>& params_r__,
140: std::vector<int>& params_i__,
141: std::ostream* pstream__ = 0) const {
142:
143: typedef T__ local_scalar_t__;
144:
145: local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
146: (void) DUMMY_VAR__; // dummy to suppress unused var warning
147:
148: T__ lp__(0.0);
149: stan::math::accumulator<T__> lp_accum__;
150: try {
151: stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
152:
153: // model parameters
154: current_statement_begin__ = 1;
155: local_scalar_t__ y;
156: (void) y; // dummy to suppress unused var warning
157: if (jacobian__)
158: y = in__.scalar_constrain(lp__);
159: else
160: y = in__.scalar_constrain();
161:
162: // model body
163:
164: current_statement_begin__ = 1;
165: lp_accum__.add(normal_log<propto__>(y, y_mean, 1));
166:
167: } catch (const std::exception& e) {
168: stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
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("y");
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: typedef double local_scalar_t__;
212:
213: vars__.resize(0);
214: stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
215: static const char* function__ = "model23d979577990_16a540c6086086816528e4524def24d9_namespace::write_array";
216: (void) function__; // dummy to suppress unused var warning
217:
218: // read-transform, write parameters
219: double y = in__.scalar_constrain();
220: vars__.push_back(y);
221:
222: double lp__ = 0.0;
223: (void) lp__; // dummy to suppress unused var warning
224: stan::math::accumulator<double> lp_accum__;
225:
226: local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
227: (void) DUMMY_VAR__; // suppress unused var warning
228:
229: if (!include_tparams__ && !include_gqs__) return;
230:
231: try {
232: if (!include_gqs__ && !include_tparams__) return;
233: if (!include_gqs__) return;
234: } catch (const std::exception& e) {
235: stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
236: // Next line prevents compiler griping about no return
237: throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
238: }
239: }
240:
241: template <typename RNG>
242: void write_array(RNG& base_rng,
243: Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
244: Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
245: bool include_tparams = true,
246: bool include_gqs = true,
247: std::ostream* pstream = 0) const {
248: std::vector<double> params_r_vec(params_r.size());
249: for (int i = 0; i < params_r.size(); ++i)
250: params_r_vec[i] = params_r(i);
251: std::vector<double> vars_vec;
252: std::vector<int> params_i_vec;
253: write_array(base_rng, params_r_vec, params_i_vec, vars_vec, include_tparams, include_gqs, pstream);
254: vars.resize(vars_vec.size());
255: for (int i = 0; i < vars.size(); ++i)
256: vars(i) = vars_vec[i];
257: }
258:
259: static std::string model_name() {
260: return "model23d979577990_16a540c6086086816528e4524def24d9";
261: }
262:
263:
264: void constrained_param_names(std::vector<std::string>& param_names__,
265: bool include_tparams__ = true,
266: bool include_gqs__ = true) const {
267: std::stringstream param_name_stream__;
268: param_name_stream__.str(std::string());
269: param_name_stream__ << "y";
270: param_names__.push_back(param_name_stream__.str());
271:
272: if (!include_gqs__ && !include_tparams__) return;
273:
274: if (include_tparams__) {
275: }
276:
277: if (!include_gqs__) return;
278: }
279:
280:
281: void unconstrained_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__ << "y";
287: param_names__.push_back(param_name_stream__.str());
288:
289: if (!include_gqs__ && !include_tparams__) return;
290:
291: if (include_tparams__) {
292: }
293:
294: if (!include_gqs__) return;
295: }
296:
297: }; // model
298:
299: } // namespace
300:
301: typedef model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9 stan_model;
302:
303: #include <rstan/rstaninc.hpp>
304: /**
305: * Define Rcpp Module to expose stan_fit's functions to R.
306: */
307: RCPP_MODULE(stan_fit4model23d979577990_16a540c6086086816528e4524def24d9_mod){
308: Rcpp::class_<rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9,
309: boost::random::ecuyer1988> >("stan_fit4model23d979577990_16a540c6086086816528e4524def24d9")
310: // .constructor<Rcpp::List>()
311: .constructor<SEXP, SEXP, SEXP>()
312: // .constructor<SEXP, SEXP>()
313: .method("call_sampler",
314: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::call_sampler)
315: .method("param_names",
316: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_names)
317: .method("param_names_oi",
318: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_names_oi)
319: .method("param_fnames_oi",
320: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_fnames_oi)
321: .method("param_dims",
322: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_dims)
323: .method("param_dims_oi",
324: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_dims_oi)
325: .method("update_param_oi",
326: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::update_param_oi)
327: .method("param_oi_tidx",
328: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::param_oi_tidx)
329: .method("grad_log_prob",
330: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::grad_log_prob)
331: .method("log_prob",
332: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::log_prob)
333: .method("unconstrain_pars",
334: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::unconstrain_pars)
335: .method("constrain_pars",
336: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::constrain_pars)
337: .method("num_pars_unconstrained",
338: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::num_pars_unconstrained)
339: .method("unconstrained_param_names",
340: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::unconstrained_param_names)
341: .method("constrained_param_names",
342: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::constrained_param_names)
343: .method("standalone_gqs",
344: &rstan::stan_fit<model23d979577990_16a540c6086086816528e4524def24d9_namespace::model23d979577990_16a540c6086086816528e4524def24d9, boost::random::ecuyer1988>::standalone_gqs)
345: ;
346: }
347:
348: // declarations
349: extern "C" {
350: SEXP file23d9659a9ab6( ) ;
351: }
352:
353: // definition
354:
355: SEXP file23d9659a9ab6( ){
356: return Rcpp::wrap("16a540c6086086816528e4524def24d9");
357: }
358:
359:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file23d9659a9ab6.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_coun
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