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CmdStanR: the R interface to CmdStan
https://mc-stan.org/cmdstanr/
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-falign-functions issues when compiling a model inside a package #787

Open wlandau opened 1 year ago

wlandau commented 1 year ago

Background

I wrote a package to pre-compile CmdStan models inside other R packages. The project is not public yet, but after it goes through my company's open-source approval process (hopefully within 2 weeks), it will be available at https://github.com/wlandau/instantiate.

The goal of instantiate is to do for cmdstanr what rstantools does for rstan: in a statistical modeling R package, compile the Stan models only once and only at installation time. Besides the obvious efficiency gains, this approach will improve the tooling in large companies with centrally maintained R installations: the dedicated devops people who install all the R packages can save end-users the trouble of debugging just-in-time compilation issues.

How it works

  1. instantiate hard-codes the value of $CMDSTAN when it installs so that downstream packages do not have to worry about finding the path to CmdStan or setting environment variables.
  2. For a package with models in inst/stan/, instantiate writes configure and configure.win to make sure install.packages() finds CmdStan and compiles all the Stan models in-place.
  3. The documentation describes the Additional_repositories: https://mc-stan.org/r-packages/ approach @jgabry mentioned in https://github.com/stan-dev/cmdstanr/issues/738. (And I agree with @danielinteractive, it would be awesome if cmdstanr itself made it to CRAN!)

Issue

On my M2 MacBook, the compiler flags set by cmdstanr::cmdstan_model() are different within install.packages() vs from outside install.packages(). In the former case, my machine automatically sets -falign-functions=64, which disagrees with the alignment in the CmdStan PCH file and causes compilation to fail. How do I prevent this flag from being set? Alternatively, if there is a way to get the value of -falign-functions that CmdStan sets, I can set it manually on my end.

Reproducible example

Here is an oversimplified version of the package setup process I implemented for instantiate:

library(cmdstanr)
#> This is cmdstanr version 0.5.3
#> - CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
#> - CmdStan path: /Users/CENSORED/cmdstan
#> - CmdStan version: 2.32.2
library(usethis)
package <- tempfile()
library <- tempfile()
tmp <- capture.output(suppressMessages(create_package(package, open = FALSE)))
dir.create(library)
dir.create(file.path(package, "inst", "stan"), recursive = TRUE)
example <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
model <- file.path(package, "inst", "stan", "bernoulli.stan")
tmp <- file.copy(example, model)
command <- paste(
  "$R_HOME/bin/Rscript",
  "--vanilla -e",
  "'options(\"cmdstanr_verbose\" = TRUE);",
  "cmdstanr::cmdstan_model(\"%s\", quiet = FALSE)'"
)
lines <- sprintf(command, model)
configure <- file.path(package, "configure")
writeLines(lines, configure)
system2(command = "chmod", args = c("+x", configure))

install.packages(pkgs = package, lib = library, repos = NULL, type = "source") fails with the following:

* installing *source* package ‘file16fef785b3954’ ...
** using staged installation
Running make \
  /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41

--- Translating Stan model to C++ code ---
bin/stanc  --o=/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41.hpp /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41.stan

--- Compiling, linking C++ code ---
clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -I/opt/R/arm64/include    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header.hpp.gch -x c++ -o /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41.o /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41.hpp
error: Default alignment for functions differs in PCH file vs. current file
error: Default alignment for functions differs in PCH file vs. current file

1 error generated.
make: *** [/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41] Error 1
1 error generated.
make: *** [/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpzheQTt/model-54d27d0dfd41] Error 1

Error: An error occured during compilation! See the message above for more information.
In addition: Warning message:
CmdStan's precompiled header (PCH) files may need to be rebuilt.
If your model failed to compile please run rebuild_cmdstan().
If the issue persists please open a bug report. 
Execution halted
ERROR: configuration failed for package ‘file16fef785b3954’
* removing ‘/private/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpcnkKva/file16fef2d10f787/file16fef785b3954’
Warning in install.packages :
  installation of package ‘/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T//RtmpcnkKva/file16fef785b3954’ had non-zero exit status

So I tried manually setting -falign-functions=1, which works on my machine, but is just a temporary hack from a tool development point of view.

lines <- c("CXXFLAGS=\"$CXXFLAGS -falign-functions=1\"", lines)
writeLines(lines, configure)

After that, install.packages(pkgs = package, lib = library, repos = NULL, type = "source") still sets -falign-functions=64 but then overrides it -falign-functions=1. Compilation succeeds:

* installing *source* package ‘file16fef785b3954’ ...
** using staged installation
Running make \
  /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af

--- Translating Stan model to C++ code ---
bin/stanc  --o=/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.stan

--- Compiling, linking C++ code ---
clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -falign-functions=1 -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -I/opt/R/arm64/include    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header.hpp.gch -x c++ -o /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.o /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:38:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:38:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^

/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:170:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:194:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:170:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:194:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^

In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:55:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/elt_multiply.hpp:9:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/multiply.hpp:7:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun.hpp:124:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:192:12: warning: unused variable 'pre_mult' [-Wunused-variable]
      auto pre_mult = a2 * pow(1 - z, -1 - a2);
           ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, double, double, double, double, double, std::tuple<double, double, double, double>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^
In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:55:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/elt_multiply.hpp:9:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/multiply.hpp:7:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun.hpp:124:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:192:12: warning: unused variable 'pre_mult' [-Wunused-variable]
      auto pre_mult = a2 * pow(1 - z, -1 - a2);
           ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, double, double, double, double, double, std::tuple<double, double, double, double>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^

/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:192:12: warning: unused variable 'pre_mult' [-Wunused-variable]
      auto pre_mult = a2 * pow(1 - z, -1 - a2);
           ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, std::tuple<stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:192:12: warning: unused variable 'pre_mult' [-Wunused-variable]
      auto pre_mult = a2 * pow(1 - z, -1 - a2);
           ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, std::tuple<stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^

In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:8:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core.hpp:29:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_division.hpp:13:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_multiplication.hpp:7:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_subtraction.hpp:104:21: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
      [bvi = b.vi_, a](const auto& vi) mutable { bvi->adj_ -= vi.adj_; });
                    ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:191:50: note: in instantiation of function template specialization 'stan::math::operator-<int, nullptr>' requested here
      auto hyper2 = hypergeometric_2F1(1 + a2, 1 - a1 + b1, 1 + b1, z_euler);
                                                 ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, std::tuple<stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^
In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:8:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core.hpp:29:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_division.hpp:13:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_multiplication.hpp:7:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_subtraction.hpp:104:21: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
      [bvi = b.vi_, a](const auto& vi) mutable { bvi->adj_ -= vi.adj_; });
                    ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:191:50: note: in instantiation of function template specialization 'stan::math::operator-<int, nullptr>' requested here
      auto hyper2 = hypergeometric_2F1(1 + a2, 1 - a1 + b1, 1 + b1, z_euler);
                                                 ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, std::tuple<stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^

In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:8:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core.hpp:29:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_division.hpp:13:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_multiplication.hpp:7:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_subtraction.hpp:104:21: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
      [bvi = b.vi_, a](const auto& vi) mutable { bvi->adj_ -= vi.adj_; });
                    ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:208:38: note: in instantiation of function template specialization 'stan::math::operator-<double, nullptr>' requested here
      auto pre_mult_ab = inv(pow(1.0 - z, a2));
                                     ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, std::tuple<stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^
In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:8:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core.hpp:29:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_division.hpp:13:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_multiplication.hpp:7:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/core/operator_subtraction.hpp:104:21: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
      [bvi = b.vi_, a](const auto& vi) mutable { bvi->adj_ -= vi.adj_; });
                    ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:208:38: note: in instantiation of function template specialization 'stan::math::operator-<double, nullptr>' requested here
      auto pre_mult_ab = inv(pow(1.0 - z, a2));
                                     ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/fun/grad_2F1.hpp:307:20: note: in instantiation of function template specialization 'stan::math::internal::grad_2F1_impl<true, true, true, true, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, std::tuple<stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>, stan::math::var_value<double>>>' requested here
  return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
                   ^

In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:198:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/functor.hpp:15:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: 'unary_function<const std::error_category *, unsigned long>' is deprecated [-Wdeprecated-declarations]
        struct hash_base : std::unary_function<T, std::size_t> {};
                                ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in inIn file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:198:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/functor.hpp:15:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: 'unary_function<const std::error_category *, unsigned long>' is deprecated [-Wdeprecated-declarations]
        struct hash_base : std::unary_function<T, std::size_t> {};
                                ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in in
stantiation of template class 'boost::hash_detail::hash_base<const std::error_category *>' requested here
        : public boost::hash_detail::hash_base<T*>
                 ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class 'boost::hash<const std::error_category *>' requested here
        boost::hash<T> hasher;
                       ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:551:9: note: in instantiation of function template specialization 'boost::hash_combine<const std::error_category *>' requested here
        hash_combine(seed, &v.category());
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<const std::error_category *, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
                                                ^
stantiation of template class 'boost::hash_detail::hash_base<const std::error_category *>' requested here
        : public boost::hash_detail::hash_base<T*>
                 ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class 'boost::hash<const std::error_category *>' requested here
        boost::hash<T> hasher;
                       ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:551:9: note: in instantiation of function template specialization 'boost::hash_combine<const std::error_category *>' requested here
        hash_combine(seed, &v.category());
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<const std::error_category *, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
                                                ^

In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:100:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/lb_constrain.hpp:114:33: warning: lambda capture 'lp' is not used [-Wunused-lambda-capture]
                               [lp, arena_lb = var(lb)](auto& vi) mutable {
                                ^
In file included from /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:1:
In file included from /Users/CENSORED/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:100:
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/lb_constrain.hpp:114:33: warning: lambda capture 'lp' is not used [-Wunused-lambda-capture]
                               [lp, arena_lb = var(lb)](auto& vi) mutable {
                                ^

/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/lub_constrain.hpp:115:12: note: in instantiation of function template specialization 'stan::math::lb_constrain<stan::math::var_value<double>, int, nullptr, nullptr>' requested here
    return lb_constrain(identity_constrain(x, ub), lb, lp);
           ^
/Users/CENSORED/cmdstan/stan/src/stan/io/deserializer.hpp:441:26: note: in instantiation of function template specialization 'stan::math::lub_constrain<stan::math::var_value<double>, int, int, nullptr, nullptr>' requested here
      return stan::math::lub_constrain(this->read<Ret>(sizes...), lb, ub, lp);
                         ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:94:29: note: in instantiation of function template specialization 'stan::io::deserializer<stan::math::var_value<double>>::read_constrain_lub<stan::math::var_value<double>, false, int, int, stan::math::var_value<double>>' requested here
      theta = in__.template read_constrain_lub<local_scalar_t__,
                            ^
/Users/CENSORED/cmdstan/stan/lib/stan_math/stan/math/rev/fun/lub_constrain.hpp:115:12: note: in instantiation of function template specialization 'stan::math::lb_constrain<stan::math::var_value<double>, int, nullptr, nullptr>' requested here
    return lb_constrain(identity_constrain(x, ub), lb, lp);
           ^
/Users/CENSORED/cmdstan/stan/src/stan/io/deserializer.hpp:441:26: note: in instantiation of function template specialization 'stan::math::lub_constrain<stan::math::var_value<double>, int, int, nullptr, nullptr>' requested here
      return stan::math::lub_constrain(this->read<Ret>(sizes...), lb, ub, lp);
                         ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:94:29: note: in instantiation of function template specialization 'stan::io::deserializer<stan::math::var_value<double>>::read_constrain_lub<stan::math::var_value<double>, false, int, int, stan::math::var_value<double>>' requested here
      theta = in__.template read_constrain_lub<local_scalar_t__,
                            ^

/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:279:12: note: in instantiation of function template specialization 'model_58822746f8af_model_namespace::model_58822746f8af_model::log_prob_impl<false, false, Eigen::Matrix<stan::math::var_value<double>, -1, 1, 0>, Eigen::Matrix<int, -1, 1, 0>, nullptr, nullptr>' requested here
    return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
           ^
/Users/CENSORED/cmdstan/stan/src/stan/model/model_base_crtp.hpp:98:50: note: in instantiation of function template specialization 'model_58822746f8af_model_namespace::model_58822746f8af_model::log_prob<false, false, stan::math::var_value<double>>' requested here
    return static_cast<const M*>(this)->template log_prob<false, false>(theta,
                                                 ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:20:3: note: in instantiation of member function 'stan::model::model_base_crtp<model_58822746f8af_model_namespace::model_58822746f8af_model>::log_prob' requested here
  ~model_58822746f8af_model() {}
  ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:279:12: note: in instantiation of function template specialization 'model_58822746f8af_model_namespace::model_58822746f8af_model::log_prob_impl<false, false, Eigen::Matrix<stan::math::var_value<double>, -1, 1, 0>, Eigen::Matrix<int, -1, 1, 0>, nullptr, nullptr>' requested here
    return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
           ^
/Users/CENSORED/cmdstan/stan/src/stan/model/model_base_crtp.hpp:98:50: note: in instantiation of function template specialization 'model_58822746f8af_model_namespace::model_58822746f8af_model::log_prob<false, false, stan::math::var_value<double>>' requested here
    return static_cast<const M*>(this)->template log_prob<false, false>(theta,
                                                 ^
/var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.hpp:20:3: note: in instantiation of member function 'stan::model::model_base_crtp<model_58822746f8af_model_namespace::model_58822746f8af_model>::log_prob' requested here
  ~model_58822746f8af_model() {}
  ^

9 warnings generated.
9 warnings generated.

clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -falign-functions=1 -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -I/opt/R/arm64/include    -DBOOST_DISABLE_ASSERTS         -L/opt/R/arm64/lib       -Wl,-L,"/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/tbb"        /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.o src/cmdstan/main.o       -Wl,-L,"/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/CENSORED/cmdstan/stan/lib/stan_math/lib/tbb"     stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af
rm -f /var/folders/4v/vh7xp8553lsbl49svl48g7p00000gp/T/RtmpXxOUHv/model-58822746f8af.o
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);  // uniform prior on interval 0,1
  y ~ bernoulli(theta);
}
** inst
** help
No man pages found in package  ‘file16fef785b3954’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (file16fef785b3954)

Session info

R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Indiana/Indianapolis
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] usethis_2.2.1  cmdstanr_0.5.3

loaded via a namespace (and not attached):
 [1] tensorA_0.36.2       utf8_1.2.3           generics_0.1.3       xml2_1.3.4          
 [5] stringi_1.7.12       digest_0.6.31        magrittr_2.0.3       evaluate_0.21       
 [9] grid_4.3.0           fastmap_1.1.1        rprojroot_2.0.3      whisker_0.4.1       
[13] backports_1.4.1      purrr_1.0.1          fansi_1.0.4          scales_1.2.1        
[17] abind_1.4-5          cli_3.6.1            rlang_1.1.1          crayon_1.5.2        
[21] munsell_0.5.0        withr_2.5.0          yaml_2.3.7           tools_4.3.0         
[25] checkmate_2.2.0      dplyr_1.1.2          colorspace_2.1-0     ggplot2_3.4.2       
[29] vctrs_0.6.3          posterior_1.4.1      R6_2.5.1             lifecycle_1.0.3     
[33] stringr_1.5.0        fs_1.6.2             pkgconfig_2.0.3      desc_1.4.2          
[37] pillar_1.9.0         gtable_0.3.3         rsconnect_0.8.29     glue_1.6.2          
[41] xfun_0.39            tibble_3.2.1         tidyselect_1.2.0     rstudioapi_0.14     
[45] knitr_1.42           farver_2.1.1         htmltools_0.5.5      rmarkdown_2.23      
[49] compiler_4.3.0       roxygen2_7.2.3       distributional_0.3.2
wlandau commented 1 year ago

Update: instantiate is now available at https://github.com/wlandau/instantiate. If you are willing, it would be great to explore this pattern together.