Merge pull request #1 from SteveBronder/fix/data-checking

changes parse_data() to remove trailing double underscores

Author: hsbadr

rstan/rstan/R/misc.R

@@ -1602,8 +1602,14 @@ parse_data <- function(cppcode) {
   # pull out object names from the data block
   objects <- gsub("^.* ([0-9A-Za-z_]+).*;.*$", "\\1",
                   cppcode[private:public])
-  # get them from the calling environment
+  # Remove model internal name underscores in case of Eigen::Maps
+  objects <- gsub("([0-9A-Za-z_]+)__", "\\1", objects)
+  # Remove any bad regex matches that found the end of an Eigen::Map.
+  objects <- gsub("^[[:digit:]]+", "\\1", objects)
+  # Remove empty characters and trim whitespaces
   objects <- objects[nzchar(trimws(objects))]
+  
+  # Get them from the calling environment
   stuff <- list()
   for (int in seq_along(objects)) {
    stuff[[objects[int]]] <- dynGet(objects[int], inherits = FALSE, ifnotfound = NULL)
@@ -1706,4 +1712,3 @@ test_221 <- function(cppcode) {
   grepl("Code generated by Stan version 2.2", cppcode, fixed = TRUE) ||
   grepl("Code generated by Stan version 3", cppcode, fixed = TRUE)  
 }
-

rstan/rstan/inst/include/rstan/stan_fit.hpp

@@ -411,12 +411,12 @@ int command(stan_args& args, Model& model, Rcpp::List& holder,
                                    "model that has no parameters.");
   int refresh = args.get_refresh();
   unsigned int id = args.get_chain_id();
-  
+
   std::ostream nullout(nullptr);
   std::ostream& c_out = refresh ? Rcpp::Rcout : nullout;
   std::ostream& c_err = refresh ? rstan::io::rcerr : nullout;
 
-  stan::callbacks::stream_logger_with_chain_id 
+  stan::callbacks::stream_logger_with_chain_id
     logger(c_out, c_out, c_out, c_err, c_err, id);
 
   R_CheckUserInterrupt_Functor interrupt;
@@ -1016,7 +1016,7 @@ class stan_fit {
     get_all_flatnames(names_oi_, dims_oi_, fnames_oi_, true);
     // get_all_indices_col2row(dims_, midx_for_col2row);
   }
-  
+
   stan_fit(SEXP data, SEXP seed, SEXP cxxf) :
   data_(data),
   model_(data_, Rcpp::as<boost::uint32_t>(seed), &rstan::io::rcout),
@@ -1221,15 +1221,15 @@ class stan_fit {
     return __sexp_result;
     END_RCPP
   }
-  
+
   SEXP standalone_gqs(SEXP pars, SEXP seed) {
     BEGIN_RCPP
     Rcpp::List holder;
 
     R_CheckUserInterrupt_Functor interrupt;
     stan::callbacks::stream_logger logger(Rcpp::Rcout, Rcpp::Rcout, Rcpp::Rcout,
                                           rstan::io::rcerr, rstan::io::rcerr);
-    
+
     const Eigen::Map<Eigen::MatrixXd> draws(Rcpp::as<Eigen::Map<Eigen::MatrixXd> >(pars));
 
     std::unique_ptr<rstan_sample_writer> sample_writer_ptr;
@@ -1248,7 +1248,7 @@ class stan_fit {
                                                   gq_size,
                                                   draws.rows(), 0,
                                                   gq_idx));
-    
+
     int ret = stan::services::error_codes::CONFIG;
     ret = stan::services::standalone_generate(model_, draws,
             Rcpp::as<unsigned int>(seed), interrupt, logger, *sample_writer_ptr);