deploy: f27f0b2

DESCRIPTION

@@ -30,7 +30,8 @@ LinkingTo:
   Rcpp,
   RcppEigen,
   BH,
-  RcppParallel
+  RcppParallel,
+  rapidjsonr
 Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

R/util.R

@@ -1,26 +1,26 @@
 write_data <- function(Npars, finite_diff, lower_bounds, upper_bounds, bounds_types, data_filepath) {
   no_bounds <- all(lower_bounds == -Inf) && all(upper_bounds == Inf)
-  dat_string <- paste0(
+  dat_string <- paste(
     '{',
-    '"Npars":', Npars, ',',
-    '"finite_diff":', finite_diff, ',',
-    '"no_bounds":', as.integer(no_bounds), ',',
-    '"lower_bounds":[', paste0(lower_bounds, collapse = ','), '],',
-    '"upper_bounds":[', paste0(upper_bounds, collapse = ','), '],',
-    '"bounds_types":[', paste0(bounds_types, collapse = ','), ']',
+    '"Npars" : ', Npars, ',',
+    '"finite_diff" : ', finite_diff, ',',
+    '"no_bounds" : ', as.integer(no_bounds), ',',
+    '"lower_bounds" : [', paste0(lower_bounds, collapse = ','), '],',
+    '"upper_bounds" : [', paste0(upper_bounds, collapse = ','), '],',
+    '"bounds_types" : [', paste0(bounds_types, collapse = ','), ']',
     '}'
   )
-  cat(dat_string, file = data_filepath)
+  writeLines(dat_string, con = data_filepath)
   invisible(NULL)
 }
 
 write_inits <- function(inits, init_filepath) {
-  dat_string <- paste0(
+  dat_string <- paste(
     '{',
-    '"pars":[', paste0(inits, collapse = ','), ']',
+    '"pars" : [', paste0(inits, collapse = ','), ']',
     '}'
   )
-  cat(dat_string, file = init_filepath)
+  writeLines(dat_string, con = init_filepath)
   invisible(NULL)
 }
 

README.md

@@ -18,14 +18,6 @@ provide a function for analytical calculation.
 
 ## Installation
 
-You can install pre-built binaries using:
-
-``` r
-# we recommend running this is a fresh R session or restarting your current session
-install.packages("StanEstimators", 
-                 repos = c("https://andrjohns.github.io/StanEstimators/", getOption("repos")))
-```
-
 Or you can build from source using:
 
 ``` r

bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES

@@ -1,7 +1,7 @@
 Package: StanEstimators
 Version: 0.0.0.9000
 Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
-LinkingTo: Rcpp, RcppEigen, BH, RcppParallel
+LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
-MD5sum: 82d792fb542890c43034a2255d57b0ef
+MD5sum: 311eb91c5636f71f94276f5bf59e15ec

bin/macosx/contrib/4.2/PACKAGES

@@ -1,7 +1,7 @@
 Package: StanEstimators
 Version: 0.0.0.9000
 Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
-LinkingTo: Rcpp, RcppEigen, BH, RcppParallel
+LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
-MD5sum: bf0926fec280104551e92f20cc56d549
+MD5sum: 49499bc184ea8294a2a297bf9164403e

bin/windows/contrib/4.2/PACKAGES

@@ -1,7 +1,7 @@
 Package: StanEstimators
 Version: 0.0.0.9000
 Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
-LinkingTo: Rcpp, RcppEigen, BH, RcppParallel
+LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
 Archs: x64

bin/windows/contrib/4.3/PACKAGES

@@ -1,7 +1,7 @@
 Package: StanEstimators
 Version: 0.0.0.9000
 Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
-LinkingTo: Rcpp, RcppEigen, BH, RcppParallel
+LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
 Archs: x64

inst/include/cmdstan/command.hpp

@@ -90,7 +90,6 @@ stan::math::mpi_cluster &get_mpi_cluster() {
 #endif
 
 int command(int argc, const char *argv[]) {
-  Rcpp::Rcout << "a" << std::endl;
   stan::callbacks::stream_writer info(Rcpp::Rcout);
   stan::callbacks::stream_writer err(Rcpp::Rcerr);
   stan::callbacks::stream_logger logger(Rcpp::Rcout, Rcpp::Rcout, Rcpp::Rcout,
@@ -154,18 +153,15 @@ int command(int argc, const char *argv[]) {
       throw std::invalid_argument(thread_msg.str());
     }
   }
-  Rcpp::Rcout << "b" << std::endl;
   stan::math::init_threadpool_tbb(num_threads);
 
   unsigned int num_chains = get_num_chains(parser);
   check_file_config(parser);
-  Rcpp::Rcout << "c" << std::endl;
 
   parser.print(info);
   write_parallel_info(info);
   write_opencl_device(info);
   info();
-  Rcpp::Rcout << "d" << std::endl;
 
   // General config for all methods
   unsigned int id = get_arg_val<int_argument>(parser, "id");
@@ -175,21 +171,17 @@ int command(int argc, const char *argv[]) {
   //////////////////////////////////////////////////
   //                Initialize Model              //
   //////////////////////////////////////////////////
-  Rcpp::Rcout << "e" << std::endl;
   arg_seed *random_arg
       = dynamic_cast<arg_seed *>(parser.arg("random")->arg("seed"));
   unsigned int random_seed = random_arg->random_value();
 
   std::string filename = get_arg_val<string_argument>(parser, "data", "file");
 
-  Rcpp::Rcout << "f" << std::endl;
   std::shared_ptr<stan::io::var_context> var_context
       = get_var_context(filename);
 
-  Rcpp::Rcout << "g" << std::endl;
   stan::model::model_base &model
       = new_model(*var_context, random_seed, &Rcpp::Rcout);
-  Rcpp::Rcout << "h" << std::endl;
 
   // Setup callbacks
   stan::callbacks::interrupt interrupt;
@@ -204,11 +196,9 @@ int command(int argc, const char *argv[]) {
   std::vector<stan::callbacks::json_writer<std::ofstream>>
       diagnostic_json_writers;
 
-  Rcpp::Rcout << "i" << std::endl;
   init_callbacks(parser, sample_writers, diagnostic_csv_writers,
                  diagnostic_json_writers);
 
-  Rcpp::Rcout << "j" << std::endl;
   // Setup initial parameter values - arg "init"
   // arg is either filename or init radius value
   std::string init = get_arg_val<string_argument>(parser, "init");
@@ -219,13 +209,10 @@ int command(int argc, const char *argv[]) {
   } catch (const std::logic_error &e) {
   }
 
-  Rcpp::Rcout << "k" << std::endl;
   std::vector<std::shared_ptr<stan::io::var_context>> init_contexts
       = get_vec_var_context(init, num_chains, id);
-  Rcpp::Rcout << "l" << std::endl;
   std::vector<std::string> model_compile_info = model.model_compile_info();
 
-  Rcpp::Rcout << "m" << std::endl;
   for (int i = 0; i < num_chains; ++i) {
     write_stan(sample_writers[i]);
     write_model(sample_writers[i], model.model_name());
@@ -238,7 +225,6 @@ int command(int argc, const char *argv[]) {
     write_model(diagnostic_csv_writers[i], model.model_name());
     parser.print(diagnostic_csv_writers[i]);
   }
-  Rcpp::Rcout << "n" << std::endl;
 
   //////////////////////////////////////////////////
   //            Invoke Services                   //
@@ -474,14 +460,12 @@ int command(int argc, const char *argv[]) {
                 tol_rel_grad, tol_param, num_iterations, save_iterations,
                 refresh, interrupt, logger, init_writers[0], sample_writers[0]);
       } else {
-  Rcpp::Rcout << "o" << std::endl;
         return_code
             = stan::services::optimize::lbfgs<stan::model::model_base, false>(
                 model, *(init_contexts[0]), random_seed, id, init_radius,
                 history_size, init_alpha, tol_obj, tol_rel_obj, tol_grad,
                 tol_rel_grad, tol_param, num_iterations, save_iterations,
                 refresh, interrupt, logger, init_writers[0], sample_writers[0]);
-  Rcpp::Rcout << "p" << std::endl;
       }
     }
     // ---- optimize end ---- //

inst/include/cmdstan/command_helper.hpp

@@ -174,19 +174,13 @@ using shared_context_ptr = std::shared_ptr<stan::io::var_context>;
  * @param file A system file to read from
  */
 inline shared_context_ptr get_var_context(const std::string &file) {
-  Rcpp::Rcout << "f1" << std::endl;
   if (file.empty()) {
     return std::make_shared<stan::io::empty_var_context>();
   }
-  Rcpp::Rcout << "f2" << std::endl;
-  std::fstream stream(file.c_str(), std::fstream::in);
-  Rcpp::Rcout << "f3" << std::endl;
+  std::ifstream stream = safe_open(file);
   if (get_suffix(file) == ".json") {
-  Rcpp::Rcout << "f4" << std::endl;
     stan::json::json_data var_context(stream);
-  Rcpp::Rcout << "f5" << std::endl;
     return std::make_shared<stan::json::json_data>(var_context);
-  Rcpp::Rcout << "f6" << std::endl;
   }
   Rcpp::Rcerr
       << "Warning: file '" << file

inst/include/stan/io/json/json_data.hpp

@@ -71,11 +71,8 @@ class json_data : public stan::io::var_context {
    * @throws json_exception if data is not well-formed stan data declaration
    */
   explicit json_data(std::istream &in) : vars_r_(), vars_i_() {
-  Rcpp::Rcout << "f41" << std::endl;
     json_data_handler handler(vars_r_, vars_i_);
-  Rcpp::Rcout << "f42" << std::endl;
     rapidjson_parse(in, handler);
-  Rcpp::Rcout << "f43" << std::endl;
   }
 
   /**

inst/include/stan/io/json/json_data_handler.hpp

@@ -457,17 +457,13 @@ class json_data_handler : public stan::json::json_handler {
    *  but we still need to track the number of tuple slots.
    */
   void key(const std::string& key) {
-    Rcpp::Rcout << "f423.9.5.6.1.9.1" << std::endl;
     if (event != meta_event::OBJ_OPEN) {
-    Rcpp::Rcout << "f423.9.5.6.1.9.2" << std::endl;
       save_key_value_pair();
     }
-    Rcpp::Rcout << "f423.9.5.6.1.9.3" << std::endl;
     event = meta_event::KEY;
     reset_values();
     std::string outer = key_str();
     key_stack.push_back(key);
-    Rcpp::Rcout << "f423.9.5.6.1.9.4" << std::endl;
     if (key_stack.size() == 1) {
       not_stan_var = !valid_varname(key);
     }
@@ -485,7 +481,6 @@ class json_data_handler : public stan::json::json_handler {
         tuple_slots_map[outer].slots_acc++;
       }
     }
-    Rcpp::Rcout << "f423.9.5.6.1.9.5" << std::endl;
     std::string vname = key_str();
     if (slot_types_map.count(vname) == 0) {
       slot_types_map[vname] = meta_type::SCALAR;

inst/include/stan/io/json/rapidjson_parser.hpp

@@ -109,17 +109,13 @@ struct RapidJSONHandler {
  */
 template <typename Handler>
 void rapidjson_parse(std::istream &in, Handler &handler) {
-  Rcpp::Rcout << "f421" << std::endl;
   rapidjson::Reader reader;
   RapidJSONHandler<Handler> filter(handler);
   rapidjson::IStreamWrapper isw(in);
-  Rcpp::Rcout << "f422" << std::endl;
   handler.start_text();
-  Rcpp::Rcout << "f423" << std::endl;
   if (!reader.Parse<rapidjson::kParseNanAndInfFlag
                     | rapidjson::kParseValidateEncodingFlag
                     | rapidjson::kParseFullPrecisionFlag>(isw, filter)) {
-  Rcpp::Rcout << "f424" << std::endl;
     rapidjson::ParseErrorCode err = reader.GetParseErrorCode();
     std::stringstream ss;
     ss << "Error in JSON parsing " << std::endl
@@ -131,7 +127,6 @@ void rapidjson_parse(std::istream &in, Handler &handler) {
     }
     throw json_error(ss.str());
   }
-  Rcpp::Rcout << "f425" << std::endl;
   handler.end_text();
 }
 }  // namespace json

inst/upgrade_headers.sh

@@ -8,7 +8,6 @@ mkdir -p include
 
 cp -r cmdstan-$CMDSTAN_VER/src/cmdstan include/cmdstan
 cp -r cmdstan-$CMDSTAN_VER/stan/src/stan include/stan
-cp -r cmdstan-$CMDSTAN_VER/stan/lib/rapidjson*/* include/rapidjson
 cp -r cmdstan-$CMDSTAN_VER/stan/lib/stan_math/stan/math include/stan/math
 cp -r cmdstan-$CMDSTAN_VER/stan/lib/stan_math/stan/math.hpp include/stan/math.hpp
 rm -rf include/stan/math/opencl

src/Makevars

@@ -1,6 +1,5 @@
 PKG_CPPFLAGS = -I"../inst/include" -I"../inst/include/sundials" -D_REENTRANT -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1
 PKG_CPPFLAGS += -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0 -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
 PKG_CPPFLAGS += $(shell "${R_HOME}/bin/Rscript" -e "RcppParallel::CxxFlags()" | tail -n 1)
-PKG_CXXFLAGS += -g -O0
 PKG_LIBS = $(shell "${R_HOME}/bin/Rscript" -e "RcppParallel::RcppParallelLibs()" | tail -n 1)
 CXX_STD = CXX17

src/contrib/PACKAGES

@@ -1,8 +1,8 @@
 Package: StanEstimators
 Version: 0.0.0.9000
 Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
-LinkingTo: Rcpp, RcppEigen, BH, RcppParallel
+LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
-MD5sum: dc0f1abdc9e6bd828feb4d99eefaedb4
+MD5sum: c6b4ffdce3d4b58366ac9439eee02b61
 NeedsCompilation: yes