Error in cmdstanr after installing cmdstanr

Interfaces CmdStan
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1

I have an error when I try to use “cmdstanr”. Although I could have installed and check the version of cmdstanr.

The code is below.

install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
library(rstan)
library(cmdstanr)
check_cmdstan_toolchain(fix = TRUE)
install_cmdstan(cores = 2)
cmdstan_version()   # I can check the version of cmdstan

model <- cmdstan_model(write_stan_file("parameters{real m;}model{5~normal(m,1);} "))      # error occurs
model$sample()

The results is below.

> install_cmdstan(cores = 2)
The C++ toolchain required for CmdStan is setup properly!
* Latest CmdStan release is v2.32.1
* Installing CmdStan v2.32.1 in C:\Users\d21601\Documents/.cmdstan/cmdstan-2.32.1
* Downloading cmdstan-2.32.1.tar.gz from GitHub...
 警告メッセージ: 
1:  readChar(make_local_path, file.info(make_local_path)$size) で: 
   UTF-8 以外のマルチバイトロケールではバイト型でのみ読み込み可能です 
2: An installation already exists at C:\Users\d21601\Documents/.cmdstan/cmdstan-2.32.1. Please remove or rename the installation folder or set overwrite=TRUE. 

> cmdstan_version()   # check version
[1] "2.32.1"

> model <- cmdstan_model(write_stan_file("parameters{real m;}model{5~normal(m,1);} "))
Compiling Stan program...
情報: 与えられたパターンのファイルが見つかりませんでした。

In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array/multi_array_ref.hpp:32,

~(omit some sentences.)~

mingw32-make: *** [make/program:14: src/cmdstan/main.o] Error 1

 エラー: An error occured during compilation! See the message above for more information.
  • Operating System: mingw32
  • language: R version 4.2.1
  • Rtools: rtools42
  • CmdStan Version: “2.32.1”
  • Compiler/Toolkit:

If a lack of information exist, please tell me. Thanks in advance.

2

I don’t know exactly the error, but the string “5~” in the model code looks strange to me

3

Thank you for replying.
I followed the example of this URL.
I just want to check if ‘cmdstanr’ works well or not.

4

Are you able to share the full output without anything cut out?

5

I’m sorry I’m late.
All error messages are below.

Compiling Stan program...
情報: 与えられたパターンのファイルが見つかりませんでした。

In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array/multi_array_ref.hpp:32,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array.hpp:34,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:63,
                 from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9,
                 from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from stan/lib/stan_math/stan/math/prim/functor.hpp:15,
                 from stan/lib/stan_math/stan/math/prim.hpp:15,
                 from stan/src/stan/io/dump.hpp:7,
                 from src/cmdstan/command_helper.hpp:5,
                 from src/cmdstan/command.hpp:14,
                 from src/cmdstan/main.cpp:1:
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:180:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  180 |         : public boost::functional::detail::unary_function<typename unary_traits<Predicate>::argument_type,bool>
      |                                             ^~~~~~~~~~~~~~

In file included from C:/rtools42/ucrt64/include/c++/13.1.0/string:49,
                 from C:/rtools42/ucrt64/include/c++/13.1.0/bits/locale_classes.h:40,
                 from C:/rtools42/ucrt64/include/c++/13.1.0/bits/ios_base.h:41,
                 from C:/rtools42/ucrt64/include/c++/13.1.0/streambuf:43,
                 from C:/rtools42/ucrt64/include/c++/13.1.0/bits/streambuf_iterator.h:35,
                 from C:/rtools42/ucrt64/include/c++/13.1.0/iterator:66,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_traits.hpp:10,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:26,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30,
                 from stan/src/stan/callbacks/writer.hpp:4,
                 from src/cmdstan/arguments/argument.hpp:4,
                 from src/cmdstan/arguments/categorical_argument.hpp:4,
                 from src/cmdstan/arguments/arg_data.hpp:4,
                 from src/cmdstan/command.hpp:4:
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~

stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:214:45: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  214 |         : public boost::functional::detail::binary_function<
      |                                             ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:252:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  252 |         : public boost::functional::detail::unary_function<
      |                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:299:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  299 |         : public boost::functional::detail::unary_function<
      |                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:345:57: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  345 |     class mem_fun_t : public boost::functional::detail::unary_function<T*, S>
      |                                                         ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:361:58: warnin
g: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  361 |     class mem_fun1_t : public boost::functional::detail::binary_function<T*, A, S>
      |                                                          ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:377:63: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  377 |     class const_mem_fun_t : public boost::functional::detail::unary_function<const T*, S>
      |                                                               ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~

stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:393:64: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  393 |     class const_mem_fun1_t : public boost::functional::detail::binary_function<const T*, A, S>
      |                                                                ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:438:61: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  438 |     class mem_fun_ref_t : public boost::functional::detail::unary_function<T&, S>
      |                                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:454:62: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  454 |     class mem_fun1_ref_t : public boost::functional::detail::binary_function<T&, A, S>
      |                                                              ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:470:67: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  470 |     class const_mem_fun_ref_t : public boost::functional::detail::unary_function<const T&, S>
      |                                                                   ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl
_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:487:68: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  487 |     class const_mem_fun1_ref_t : public boost::functional::detail::binary_function<const T&, A, S>
      |                                                                    ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:533:73: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  533 |     class pointer_to_unary_function : public boost::functional::detail::unary_function<Arg,Result>
      |                                                                         ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:557:74: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  557 |     class pointer_to_binary_function : public boost::functional::detail::binary_function<Arg1,Arg2,Result>
      |                                                                          ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/13.1.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~

In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:74,
                 from stan/lib/stan_math/stan/math/rev.hpp:10,
                 from stan/src/stan/model/log_prob_grad.hpp:4,
                 from src/cmdstan/command_helper.hpp:10:
stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp: In function 'auto stan::math::generalized_inverse(const VarMat&)':
stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp:67: note: '-Wmisleading-indentation' is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers
   67 |   if (G.size() == 0)
      | 

stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp:67: note: adding '-flarge-source-files' will allow for more column-tracking support, at the expense of compilation time and memory

mingw32-make: *** [make/program:14: src/cmdstan/main.o] Error 1

 エラー: An error occured during compilation! See the message above for more information.
6

I would recommend to reinstall cmdstan and check if the bernoulli code can be compiled without errors (it looks like it was not installed properly)

7

Hiroki, I have the same problem as yours. Have you figured out a solution?

8

I referred the following page.
I guess that this problem occurs when you can’t set the PATH of the Rtools4.2.