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Error installing rstan on macOS Ventura 13.4 with arm64 architecture: Need assistance with C++ compilation #1077

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truenomad opened this issue Jun 19, 2023 · 7 comments
Closed

Error installing rstan on macOS Ventura 13.4 with arm64 architecture: Need assistance with C++ compilation #1077

truenomad opened this issue Jun 19, 2023 · 7 comments

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@truenomad
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truenomad commented Jun 19, 2023 •
edited

Summary:

I have been attempting to install rstan on macOS Ventura 13.4 with arm64 architecture, following the guide provided in the official rstan GitHub repository (https://github.com/stan-dev/rstan/wiki/Installing-RStan-from-Source#mac). My system has Xcode and command line tools version 14.3.1, as well as Clang version 14.0.3.

I suspect that the error is related to the C++ code that rstan attempts to compile, but I am uncertain about the appropriate steps to take from here. I have tried various solutions suggested in Stack Overflow threads without any success. Some of the threads I have explored include:

https://apple.stackexchange.com/questions/458062/unable-to-find-include-file-on-newly-updated-macosc-c

https://stackoverflow.com/questions/75921280/updating-to-macos-13-3-broke-compiling-cpp

Reproducible Steps:

Here is the code I have used for installation:

install.packages("rstan", type = "source”)

Unfortunately, the package does not download successfully and produces the following error:

trying URL 'http://cran.us.r-project.org/src/contrib/rstan_2.21.8.tar.gz'
Content type 'application/x-gzip' length 1203455 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++14
using SDK: ‘’
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS   -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -O3 -mtune=native -arch arm64 -ftemplate-depth-256 -c Module.cpp -o Module.o
In file included from Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:310:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:310:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {};
                                                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {};
                                                ^~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl       : public false_type {};
                ^
In file included from Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:517:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/is_permutation.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/advance.h:19:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__utility/unreachable.h:13:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:123:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:339:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:523:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:25:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:848:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/new:94:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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_() {}
                                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
                       ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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_() {}
    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
                                    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:523:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:25:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:848:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/new:94:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:523:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:25:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
  ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
#    define _LIBCPP_CONSTEXPR constexpr
                              ^
In file included from Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:523:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:25:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
  ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
#    define _LIBCPP_CONSTEXPR constexpr
                              ^
In file included from Module.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:523:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:25:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
             ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
                       ^ ~~~~~~~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
                                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
           ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [Module.o] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan’
Warning in install.packages :
  installation of package ‘rstan’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/tj/gxsjjg6x3z3g43qcm49tmfmh0000gn/T/Rtmp38B6Sd/downloaded_packages’

RStan Version: 2.21.8

R Version: 4.3.1

The version of R you are running (e.g., from R.version.string)

Operating System: M2 Mac with macOS Ventura 13.4 with arm64

R session Info:

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

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: Europe/London
tzcode source: internal

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

loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1
@bob-carpenter
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bob-carpenter commented Jun 20, 2023 •
edited

If you only need to run Stan models and don't need to build a binary package or access log densities and gradients, you might want to try cmdstanr. It's easier to install and more up-to-date with Stan. RStan is being updated and the plan is to bring the CRAN version up to date in the immediate future, but it's a painstaking process with all the dependent packages and CRAN rules.

@truenomad
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Author

Hi @bob-carpenter
Thanks for the response. I have already tried cmdstanr and the same issue arises when trying to compile models. Not sure what is going.

install_cmdstan(cores = 10)
`The C++ toolchain required for CmdStan is setup properly!

  • Latest CmdStan release is v2.32.2
  • Installing CmdStan v2.32.2 in /Users/mohamedyusuf/.cmdstan/cmdstan-2.32.2
  • Downloading cmdstan-2.32.2.tar.gz from GitHub...
    Warning message:
    An installation already exists at /Users/mohamedyusuf/.cmdstan/cmdstan-2.32.2. Please remove or rename the installation folder or set overwrite=TRUE.`
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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:679:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__debug:15:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:679:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__debug:16:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {};
                                                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
temp
late <>          struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
                                                ^~~~~~~~~

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:684:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/common_iterator.h:22:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/variant:214:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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_() {}
                                            ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
                       ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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_() {}
    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
                                    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:684:
In file included from /Applications/Xcode.app/Contents/Developer/
Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/common_iterator.h:22:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/variant:214:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
  ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
  _LIBCPP_CONSTEXPR u
nique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
                                         ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
  ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Applications
/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:860:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
                               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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()) {}
                                         ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
                        ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
             ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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 {
                       ^ ~~~~~~~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
                                            ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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
           ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/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_opencl.o] Error 1

Error: An error occured during compilation! See the message above for more information.
>

@bob-carpenter
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I have no idea what's going on here, but it looks like a problem with OpenCL, which is what we use for GPU support. I'm pinging a few people who may know what's going on: @jgabry @SteveBronder @bgoodri.

@truenomad
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I have no idea what's going on here, but it looks like a problem with OpenCL, which is what we use for GPU support. I'm pinging a few people who may know what's going on: @jgabry @SteveBronder @bgoodri.

Still struggling with this issue. Wonder if anyone mentioned here can help .

@jamesmbaazam
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jamesmbaazam commented Sep 11, 2023 •
edited

HI @truenomad, I might have encountered a similar issue in the recent past, which was solved here stan-dev/cmdstanr#790. Try and follow the conversation and see if it helps.

@truenomad
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HI @truenomad, I might have encountered a similar in the recent past, which was solved here stan-dev/cmdstanr#790. Try and follow the conversation and see if it helps.

This solves it !! Thank you so much.

@jamesmbaazam
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@truenomad Glad it helped.

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@bob-carpenter @truenomad @jamesmbaazam