Compilation issue

Developers
1

Hello, I have been very happy using Stan, but now, with a new computer (MacOS Big Sur Version 11.2), I am running into trouble compiling my model using Pystan. I am able to import the package in python, but once I compile the C++ code, I receive the error message ``CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed with exit status 254’’. The entire, very long error message is below. I have tried solutions given on other forums, but none have yet worked.
Thank you very much in advance!

DIAGNOSTIC(S) FROM PARSER:
Info:
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
resid_q[i] ~ normal(…)
Info:
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
resid_theta[i] ~ normal(…)

clang-10: warning: -Wl,-export_dynamic: ‘linker’ input unused [-Wunused-command-line-argument]
In file included from /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp:63:
/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:14:2: error: “Something’s broken. UCHAR_MAX should be defined in limits.h.”
#error “Something’s broken. UCHAR_MAX should be defined in limits.h.”
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:18:2: error: “Python’s source code assumes C’s unsigned char is an 8-bit type.”
#error “Python’s source code assumes C’s unsigned char is an 8-bit type.”
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:27:5: error: “Python.h requires that stdio.h define NULL.”

error “Python.h requires that stdio.h define NULL.”

^

In file included from /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp:63:
In file included from /Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:30:
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:73:64: error: use of undeclared identifier ‘strchr’
char* __libcpp_strchr(const char* __s, int __c) {return (char*)strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:80:75: error: use of undeclared identifier ‘strpbrk’
char* __libcpp_strpbrk(const char* __s1, const char* __s2) {return (char*)strpbrk(__s1, __s2);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:87:65: error: use of undeclared identifier ‘strrchr’; did you mean ‘strchr’?
char* __libcpp_strrchr(const char* __s, int __c) {return (char*)strrchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:75:13: note: ‘strchr’ declared here
const char* strchr(const char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:94:49: error: unknown type name ‘size_t’
void* __libcpp_memchr(const void* __s, int __c, size_t __n) {return (void*)memchr(__s, __c, __n);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:96:46: error: unknown type name ‘size_t’
const void* memchr(const void* __s, int __c, size_t __n) {return __libcpp_memchr(__s, __c, __n);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:98:46: error: unknown type name ‘size_t’
void* memchr( void* __s, int __c, size_t __n) {return __libcpp_memchr(__s, __c, __n);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:101:74: error: use of undeclared identifier ‘strstr’; did you mean ‘strchr’?
char* __libcpp_strstr(const char* __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:77:13: note: ‘strchr’ declared here
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:101:74: error: no matching function for call to ‘strchr’
char* __libcpp_strstr(const char* __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:77:13: note: candidate disabled:
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:101:81: error: cannot initialize a parameter of type 'char ’ with an lvalue of type 'const char ’
char __libcpp_strstr(const char __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^~~~
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:77:32: note: passing argument to parameter ‘__s’ here
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
In file included from /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp:63:
In file included from /Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:34:
In file included from /Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/stdlib.h:100:
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:773:12: error: no member named ‘labs’ in the global namespace; did you mean ‘abs’?
return ::labs(__x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:772:39: note: ‘abs’ declared here
inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:777:12: error: no member named ‘llabs’ in the global namespace
return ::llabs(__x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:785:12: error: no member named ‘fabsf’ in the global namespace
return ::fabsf(__lcpp_x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:789:12: error: no member named ‘fabs’ in the global namespace; did you mean ‘abs’?
return ::fabs(__lcpp_x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:772:39: note: ‘abs’ declared here
inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:794:12: error: no member named ‘fabsl’ in the global namespace
return ::fabsl(__lcpp_x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:808:34: error: unknown type name ‘ldiv_t’
inline _LIBCPP_INLINE_VISIBILITY ldiv_t div(long __x, long __y) _NOEXCEPT {
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:809:12: error: no member named ‘ldiv’ in the global namespace
return ::ldiv(__x, __y);
~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
Stack dump:
0. Program arguments: x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map={SRC_DIR}=/usr/local/src/conda/{PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/annalea_albright/opt/anaconda3/envs/bayesian=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/annalea_albright/opt/anaconda3/envs/bayesian/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/annalea_albright/opt/anaconda3/envs/bayesian/include -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk -Iopt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/src -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/numpy/core/include -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8 -c /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp -o /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y

  1. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:169:74: current parser token ‘type’
  2. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:19:1: parsing namespace ‘boost’
  3. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:21:1: parsing namespace ‘boost::units’
  4. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:26:1: parsing namespace ‘boost::units::detail’
  5. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:163:1: parsing struct/union/class body ‘boost::units::detail::static_int_power_sign_impl<N, true>’
  6. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:166:5: parsing struct/union/class body ‘boost::units::detail::static_int_power_sign_impl<N, true>::apply’
    0 libLLVM-10.dylib 0x000000010ead5765 llvm::sys::PrintStackTrace(llvm::raw_ostream&) + 37
    1 libLLVM-10.dylib 0x000000010ead4668 llvm::sys::RunSignalHandlers() + 248
    2 libLLVM-10.dylib 0x000000010ead4d32 llvm::sys::CleanupOnSignal(unsigned long) + 210
    3 libLLVM-10.dylib 0x000000010ea185ad CrashRecoverySignalHandler(int) + 189
    4 libsystem_platform.dylib 0x00007fff2038ed7d _sigtramp + 29
    5 libclang-cpp.10.dylib 0x0000000108f4e62e clang::Sema::BuildDeclarationNameExpr(clang::CXXScopeSpec const&, clang::LookupResult&, bool, bool) + 670
    clang-10: error: clang frontend command failed due to signal (use -v to see invocation)
    clang version 10.0.0
    Target: x86_64-apple-darwin13.4.0
    Thread model: posix
    InstalledDir: /Users/annalea_albright/opt/anaconda3/envs/bayesian/bin
    clang-10: note: diagnostic msg: PLEASE submit a bug report to and include the crash backtrace, preprocessed source, and associated run script.
    Traceback (most recent call last):

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/unixccompiler.py”, line 117, in _compile
self.spawn(compiler_so + cc_args + [src, ‘-o’, obj] +

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/ccompiler.py”, line 910, in spawn
spawn(cmd, dry_run=self.dry_run)

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/spawn.py”, line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/spawn.py”, line 157, in _spawn_posix
raise DistutilsExecError(

DistutilsExecError: command ‘x86_64-apple-darwin13.4.0-clang’ failed with exit status 254

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/Users/annalea_albright/Dropbox/EUREC4A/Conceptual_Model/bayesian/joint_inversion_A_Cth.py”, line 215, in
sm = pystan.StanModel(file,

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/model.py”, line 378, in init
build_extension.run()

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/command/build_ext.py”, line 340, in run
self.build_extensions()

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/command/build_ext.py”, line 449, in build_extensions
self._build_extensions_serial()

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/command/build_ext.py”, line 474, in _build_extensions_serial
self.build_extension(ext)

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/command/build_ext.py”, line 528, in build_extension
objects = self.compiler.compile(sources,

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/ccompiler.py”, line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)

File “/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/distutils/unixccompiler.py”, line 120, in _compile
raise CompileError(msg)

CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed with exit status 254

DIAGNOSTIC(S) FROM PARSER:
Info:
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
resid_q[i] ~ normal(…)
Info:
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
resid_theta[i] ~ normal(…)

clang-10: warning: -Wl,-export_dynamic: ‘linker’ input unused [-Wunused-command-line-argument]
In file included from /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp:63:
/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:14:2: error: “Something’s broken. UCHAR_MAX should be defined in limits.h.”
#error “Something’s broken. UCHAR_MAX should be defined in limits.h.”
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:18:2: error: “Python’s source code assumes C’s unsigned char is an 8-bit type.”
#error “Python’s source code assumes C’s unsigned char is an 8-bit type.”
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:27:5: error: “Python.h requires that stdio.h define NULL.”

error “Python.h requires that stdio.h define NULL.”

^

In file included from /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp:63:
In file included from /Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:30:
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:73:64: error: use of undeclared identifier ‘strchr’
char* __libcpp_strchr(const char* __s, int __c) {return (char*)strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:80:75: error: use of undeclared identifier ‘strpbrk’
char* __libcpp_strpbrk(const char* __s1, const char* __s2) {return (char*)strpbrk(__s1, __s2);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:87:65: error: use of undeclared identifier ‘strrchr’; did you mean ‘strchr’?
char* __libcpp_strrchr(const char* __s, int __c) {return (char*)strrchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:75:13: note: ‘strchr’ declared here
const char* strchr(const char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:94:49: error: unknown type name ‘size_t’
void* __libcpp_memchr(const void* __s, int __c, size_t __n) {return (void*)memchr(__s, __c, __n);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:96:46: error: unknown type name ‘size_t’
const void* memchr(const void* __s, int __c, size_t __n) {return __libcpp_memchr(__s, __c, __n);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:98:46: error: unknown type name ‘size_t’
void* memchr( void* __s, int __c, size_t __n) {return __libcpp_memchr(__s, __c, __n);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:101:74: error: use of undeclared identifier ‘strstr’; did you mean ‘strchr’?
char* __libcpp_strstr(const char* __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:77:13: note: ‘strchr’ declared here
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:101:74: error: no matching function for call to ‘strchr’
char* __libcpp_strstr(const char* __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:77:13: note: candidate disabled:
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:101:81: error: cannot initialize a parameter of type 'char ’ with an lvalue of type 'const char ’
char __libcpp_strstr(const char __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^~~~
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/string.h:77:32: note: passing argument to parameter ‘__s’ here
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
In file included from /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp:63:
In file included from /Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8/Python.h:34:
In file included from /Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/stdlib.h:100:
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:773:12: error: no member named ‘labs’ in the global namespace; did you mean ‘abs’?
return ::labs(__x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:772:39: note: ‘abs’ declared here
inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:777:12: error: no member named ‘llabs’ in the global namespace
return ::llabs(__x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:785:12: error: no member named ‘fabsf’ in the global namespace
return ::fabsf(__lcpp_x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:789:12: error: no member named ‘fabs’ in the global namespace; did you mean ‘abs’?
return ::fabs(__lcpp_x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:772:39: note: ‘abs’ declared here
inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:794:12: error: no member named ‘fabsl’ in the global namespace
return ::fabsl(__lcpp_x);
~~^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:808:34: error: unknown type name ‘ldiv_t’
inline _LIBCPP_INLINE_VISIBILITY ldiv_t div(long __x, long __y) _NOEXCEPT {
^
/Users/annalea_albright/opt/anaconda3/envs/bayesian/bin/…/include/c++/v1/math.h:809:12: error: no member named ‘ldiv’ in the global namespace
return ::ldiv(__x, __y);
~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
Stack dump:
0. Program arguments: x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map={SRC_DIR}=/usr/local/src/conda/{PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/annalea_albright/opt/anaconda3/envs/bayesian=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/annalea_albright/opt/anaconda3/envs/bayesian/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/annalea_albright/opt/anaconda3/envs/bayesian/include -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk -Iopt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/src -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/numpy/core/include -I/Users/annalea_albright/opt/anaconda3/envs/bayesian/include/python3.8 -c /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.cpp -o /var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/var/folders/8t/v51849h92dsb7qvyx0cxz_d40000gn/T/pystan_r125f1rk/stanfit4anon_model_ca7796d6d6cd0b8fb0ccbed2777eb05e_4452662775328707948.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y

  1. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:169:74: current parser token ‘type’
  2. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:19:1: parsing namespace ‘boost’
  3. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:21:1: parsing namespace ‘boost::units’
  4. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:26:1: parsing namespace ‘boost::units::detail’
  5. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:163:1: parsing struct/union/class body ‘boost::units::detail::static_int_power_sign_impl<N, true>’
  6. /Users/annalea_albright/opt/anaconda3/envs/bayesian/lib/python3.8/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/units/detail/static_rational_power.hpp:166:5: parsing struct/union/class body ‘boost::units::detail::static_int_power_sign_impl<N, true>::apply’
    0 libLLVM-10.dylib 0x000000010ead5765 llvm::sys::PrintStackTrace(llvm::raw_ostream&) + 37
    1 libLLVM-10.dylib 0x000000010ead4668 llvm::sys::RunSignalHandlers() + 248
    2 libLLVM-10.dylib 0x000000010ead4d32 llvm::sys::CleanupOnSignal(unsigned long) + 210
    3 libLLVM-10.dylib 0x000000010ea185ad CrashRecoverySignalHandler(int) + 189
    4 libsystem_platform.dylib 0x00007fff2038ed7d _sigtramp + 29
    5 libclang-cpp.10.dylib 0x0000000108f4e62e clang::Sema::BuildDeclarationNameExpr(clang::CXXScopeSpec const&, clang::LookupResult&, bool, bool) + 670
    clang-10: error: clang frontend command failed due to signal (use -v to see invocation)
    clang version 10.0.0
    Target: x86_64-apple-darwin13.4.0
    Thread model: posix
    InstalledDir: /Users/annalea_albright/opt/anaconda3/envs/bayesian/bin
    clang-10: note: diagnostic msg: PLEASE submit a bug report to and include the crash backtrace, preprocessed source, and associated run script.
    clang-10: note: diagnostic msg: Error generating preprocessed source(s).
2

There is probably some clash between system compiler and anaconda compiler.

What does these give

gcc --version
which gcc
3

Thank you for your response!

gcc --version gives:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 12.0.5 (clang-1205.0.22.9)

Target: arm64-apple-darwin20.3.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

which gcc gives:
/usr/bin/gcc

4

Ok,

Have you defined CXX or CC env variables

env

Your python tries to compile with conda compiler, but is it might be missing some files.

Try to define

CC=gcc
CXX=g++
6

But I have run
env
followed by
CC=gcc
CXX=g++
then reloaded pystan, and unfortunately I still get the same error message.

7

Hello Ari, @ahartikainen

I defined CC=gcc and CXX=g++ but I still receive the same long error message including command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 254. Do you have any other ideas for how to get my program to compile? I have downloaded a clean version of anaconda and my Pystan environment. My OS is Mac Big Sur.

Thank you,
Anna Lea

8

I have the same issue, still getting the same error

9

CmdStanPy is easier to get running because it doesn’t induce a binary dependency between Python and C++. There is also a conda install for it.