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Summary

compile_model_methods = TRUE (the $log_prob() / $grad_log_prob() / $hessian() methods) and compile_standalone = TRUE (expose_functions()) currently fail to compile for any model that uses an external C++ user_header — even though the very same model samples without issue. This blocks a common workflow: validating a hand-written C++ log density / analytic gradient against the pure-Stan autodiff version via grad_log_prob().

Reproducible example

bernoulli_external.stan (declares make_odds, defined in the header):

functions { real make_odds(real theta); }
data { int<lower=0> N; array[N] int<lower=0,upper=1> y; }
parameters { real<lower=0,upper=1> theta; }
model { theta ~ beta(1, 1); y ~ bernoulli(theta); }
generated quantities { real odds = make_odds(theta); }

make_odds.hpp (in the model's namespace, per the CmdStan convention):

#include <stan/math.hpp>
#include <ostream>
namespace bernoulli_external_model_namespace {
  template <typename T0__, stan::require_all_t<stan::is_stan_scalar<T0__>>* = nullptr>
  stan::promote_args_t<T0__> make_odds(const T0__& theta, std::ostream* pstream__) {
    return theta / (1 - theta);
  }
}

mod <- cmdstan_model("bernoulli_external.stan",
                     user_header = "make_odds.hpp",
                     compile_model_methods = TRUE)

mod$sample() works, but compiling the model methods aborts with:

error: use of undeclared identifier 'make_odds'

Root cause

Two independent problems in the standalone / model-methods build path:

1. Mangled namespace. The standalone & model-methods C++ is generated by calling stanc directly through an argument vector (no shell) in get_standalone_hpp(), reusing the same --name='foo_model' flag that is built for the make-based executable build. The make path is processed by a shell that strips the quotes; the direct call is not, so the literal quotes become part of the model name, producing the namespace 'foo_model'_namespace (x39model...x39_namespace after C++ name-mangling). External C++ functions are defined by the user in foo_model_namespace, so they are not visible to the generated code.

2. Header not included. rcpp_source_stan() does not -include the user header when compiling the methods via Rcpp::sourceCpp(), unlike CmdStan's makefile, which adds -include $(USER_HEADER).

Fix

• Build an unquoted variant of the stanc options for the two direct get_standalone_hpp() calls; the make path keeps the quoted form (so names/paths with spaces are still safe there).
• Stash the user-header path on the model-methods env (and on self$functions) and force-include it in rcpp_source_stan(), mirroring CmdStan's -include $(USER_HEADER).

This also enables compile_standalone = TRUE / expose_functions() for models with external C++, which share rcpp_source_stan().

Verification

For a normal model and an identical model whose single likelihood term is routed through an external C++ function, with the fix log_prob() and grad_log_prob() match the pure-Stan autodiff version exactly:

PLAIN     log_prob=-51.45881541  grad=(22.628038, 70.420847)
EXTERNAL  log_prob=-51.45881541  grad=(22.628038, 70.420847)
max|lp diff| = 0   max|grad diff| = 0

Adds a regression test in tests/testthat/test-model-methods.R using the existing bernoulli_external fixture (full test-model-methods.R passes locally on macOS / CmdStan 2.39.0).

Copyright and Licensing

Please list the copyright holder for the work you are submitting
(this will be you or your assignee, such as a university or company):

Scott Spencer

By submitting this pull request, the copyright holder is agreeing to
license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)