Unable to compile stan models on MacOS Ventura #790
Comments
|
@jamesmbaazam Sorry for the slow reply. Does |
|
Yes, it errors too. Same errors as above. |
|
It looks like your system isn't delegating to the commandline-tools properly. Can you first check that the commandline tools are installed by opening up a terminal and running: This will either open up the installer to install the tools, or will message that they are already installed. After that, specify that the system should delegate to the command line tools by running: Then can you try starting a new R session and running the |
|
Thanks for your help so far but unfortunately, I'm still struggling. When I run /usr/local/include/stdlib.h:364:13: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]
extern char *suboptarg; /* getsubopt(3) external variable */
^
/usr/local/include/stdlib.h:364:13: note: insert '_Nullable' if the pointer may be null
extern char *suboptarg; /* getsubopt(3) external variable */
^
_Nullable
/usr/local/include/stdlib.h:364:13: note: insert '_Nonnull' if the pointer should never be null
extern char *suboptarg; /* getsubopt(3) external variable */
^
_Nonnull
193 warnings generated.
193 warnings generated.Now, when I run the following > file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
> mod <- cmdstan_model(file)I get Compiling Stan program...
error: PCH file built from a different branch () than the compiler ((clang-1403.0.22.14.1))
1
error generated.
make: *** [/var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T/RtmpWDQj0N/model-1c4858495cb4] 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. |
|
Are you using homebrew/macports and have installed another toolchain? The output is referencing files in |
|
Yes, I've installed |
|
It appears that your system isn't properly configured to handle the multiple toolchains, and there are files/libraries being included when they shouldn't. Can you try removing gcc and llvm and trying again? |
|
I just removed them and re-run the example but still getting an error as follows: > library("cmdstanr")
This is cmdstanr version 0.6.0
- CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
- CmdStan path: /Users/lshja16/.cmdstan/cmdstan-2.32.2
- CmdStan version: 2.32.2
> file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
> mod <- cmdstan_model(file)
Compiling Stan program...
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:26:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_traits.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:679:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__debug:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:26:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_traits.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:679:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__debug:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <cla
ss _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:26:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_traits.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:684:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/common_iterator.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/variant:214:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'std::exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTo
ols/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:26:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_traits.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:684:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/common_iterator.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/variant:214:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:38:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/functions.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/size.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/size_type.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/concepts.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_concepts.hpp:26:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/argum
ents/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:38:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/functions.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/size.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/size_type.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/concepts.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_concepts.hpp:26:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from src/cmdstan/main.cpp:1:
In file included from src/cmdstan/command.hpp:4:
In file included from src/cmdstan/arguments/arg_data.hpp:4:
In file included from src/cmdstan/arguments/categorical_argument.hpp:4:
In file included from src/cmdstan/arguments/argument.hpp:4:
In file included from stan/src/stan/callbacks/writer.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:38:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/functions.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/size.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/size_type.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/range/concepts.hpp:20:
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_concepts.hpp:26:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _N
OEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h
:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [src/cmdstan/main.o] Error 1
Error: An error occured during compilation! See the message above for more information. |
|
The next step is to check the include/library paths that your compiler is looking through. Can you post the output from: |
|
I get |
|
The most likely culprit is something in your What output do you get from: |
|
Oh, interesting. When I run that, I get |
|
Yep, that list includes many C/C++ library headers that are being included before the toolchain headers, breaking the imports. The fastest solution would be to delete the |
With the caveat that it might affect your other libraries, if your homebrew installation is installing in |
|
Thanks so much for your patience and help. Deleting the directory worked for me. 😄 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Describe the issue
I am unable to compile the example model that comes with the package.
Below is a reproducible example
CmdStanR version number
Your CmdStanR version number (e.g. from
packageVersion("cmdstanr")).0.5.3
Here is the results of
sessionInfo()The text was updated successfully, but these errors were encountered: