Compilation issue

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).

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

What does these give

gcc --version
which gcc

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

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++

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

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

I have the same issue, still getting the same error