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changes parse_data() to remove trailing double underscores #1

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Merged
hsbadr merged 5 commits into from
Apr 20, 2021
Merged

changes parse_data() to remove trailing double underscores #1

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34b5b8f
Update stan submodule
hsbadr Apr 20, 2021
0c2cb19
changes parse_data() for the cpp file to remove trailing double under…
SteveBronder Apr 20, 2021
871c322
update upstream to match 2.25 branch
SteveBronder Apr 20, 2021
6c22e04
update gitmodules
SteveBronder Apr 20, 2021
9ce95d5
Update rstan/rstan/R/misc.R
SteveBronder Apr 20, 2021
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9 changes: 7 additions & 2 deletions rstan/rstan/R/misc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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)
}

12 changes: 6 additions & 6 deletions rstan/rstan/inst/include/rstan/stan_fit.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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),
Expand Down Expand Up @@ -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;
Expand All @@ -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);
Expand Down