Pystan3 Not compiling with conda version of clang on mac os (can't find header files)

Interfaces PyStan
, ,
1

I am trying to run the following simple code to test out my pystan installation:

import pystan
fit = pystan.StanModel(model_code="parameters {real theta;} model {theta ~ normal(0,1);}", model_name="model_name")

I get the following output:

In file included from /var/folders/pd/ty1c08q94g51b488780wp8s80000gq/T/pystan_2mhjt8vz/stanfit4model_name_c119d6069f0316b80eefa9c12c3ce343_3927306634021715441.cpp:62:
In file included from /Users/molarinr/miniconda3/envs/res/include/python3.9/Python.h:25:
/Users/molarinr/miniconda3/envs/res/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found
#include_next <stdio.h>
              ^~~~~~~~~
Stack dump:
0.	Program arguments: /Users/molarinr/miniconda3/envs/res/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/molarinr/miniconda3/envs/res/include -arch x86_64 -I/Users/molarinr/miniconda3/envs/res/include -fPIC -O2 -isystem /Users/molarinr/miniconda3/envs/res/include -arch x86_64 -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/var/folders/pd/ty1c08q94g51b488780wp8s80000gq/T/pystan_2mhjt8vz -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/pystan -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/pystan/stan/src -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/pystan/stan/lib/stan_math -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/Users/molarinr/miniconda3/envs/res/lib/python3.9/site-packages/numpy/core/include -I/Users/molarinr/miniconda3/envs/res/include/python3.9 -c /var/folders/pd/ty1c08q94g51b488780wp8s80000gq/T/pystan_2mhjt8vz/stanfit4model_name_c119d6069f0316b80eefa9c12c3ce343_3927306634021715441.cpp -o /var/folders/pd/ty1c08q94g51b488780wp8s80000gq/T/pystan_2mhjt8vz/var/folders/pd/ty1c08q94g51b488780wp8s80000gq/T/pystan_2mhjt8vz/stanfit4model_name_c119d6069f0316b80eefa9c12c3ce343_3927306634021715441.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y 
1.	/Users/molarinr/miniconda3/envs/res/lib/python3.9/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/molarinr/miniconda3/envs/res/lib/python3.9/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/molarinr/miniconda3/envs/res/lib/python3.9/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/molarinr/miniconda3/envs/res/lib/python3.9/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/molarinr/miniconda3/envs/res/lib/python3.9/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/molarinr/miniconda3/envs/res/lib/python3.9/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         0x0000000114d7a765 llvm::sys::PrintStackTrace(llvm::raw_ostream&) + 37
1  libLLVM-10.dylib         0x0000000114d79668 llvm::sys::RunSignalHandlers() + 248
2  libLLVM-10.dylib         0x0000000114d79d32 llvm::sys::CleanupOnSignal(unsigned long) + 210
3  libLLVM-10.dylib         0x0000000114cbd5ad CrashRecoverySignalHandler(int) + 189
4  libsystem_platform.dylib 0x00007ff804e39c1d _sigtramp + 29
5  libsystem_platform.dylib 0x00007fcfc4b24ed8 _sigtramp + 18446743900833886936
6  libclang-cpp.10.dylib    0x000000010e580eae clang::Sema::CheckTemplateArgument(clang::TemplateTypeParmDecl*, clang::TypeSourceInfo*) + 206
7  libclang-cpp.10.dylib    0x000000010e59b2dd clang::Sema::CheckTemplateTypeArgument(clang::TemplateTypeParmDecl*, clang::TemplateArgumentLoc&, llvm::SmallVectorImpl<clang::TemplateArgument>&) + 1981
8  libclang-cpp.10.dylib    0x000000010e58f9bf clang::Sema::CheckTemplateArgumentList(clang::TemplateDecl*, clang::SourceLocation, clang::TemplateArgumentListInfo&, bool, llvm::SmallVectorImpl<clang::TemplateArgument>&, bool, bool*) + 975
9  libclang-cpp.10.dylib    0x000000010e58e245 clang::Sema::CheckTemplateIdType(clang::TemplateName, clang::SourceLocation, clang::TemplateArgumentListInfo&) + 741
10 libclang-cpp.10.dylib    0x000000010e00e8af clang::Sema::ActOnCXXNestedNameSpecifier(clang::Scope*, clang::CXXScopeSpec&, clang::SourceLocation, clang::OpaquePtr<clang::TemplateName>, clang::SourceLocation, clang::SourceLocation, llvm::MutableArrayRef<clang::ParsedTemplateArgument>, clang::SourceLocation, clang::SourceLocation, bool) + 1695
11 libclang-cpp.10.dylib    0x000000010d9f7592 clang::Parser::ParseOptionalCXXScopeSpecifier(clang::CXXScopeSpec&, clang::OpaquePtr<clang::QualType>, bool, bool*, bool, clang::IdentifierInfo**, bool, bool) + 1778
12 libclang-cpp.10.dylib    0x000000010da648b2 clang::Parser::TryAnnotateTypeOrScopeToken() + 194
13 libclang-cpp.10.dylib    0x000000010d9b116a clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*) + 2298
14 libclang-cpp.10.dylib    0x000000010d9d7644 clang::Parser::ParseCXXClassMemberDeclaration(clang::AccessSpecifier, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo const&, clang::ParsingDeclRAIIObject*) + 2244
15 libclang-cpp.10.dylib    0x000000010d9da152 clang::Parser::ParseCXXClassMemberDeclarationWithPragmas(clang::AccessSpecifier&, clang::Parser::ParsedAttributesWithRange&, clang::TypeSpecifierType, clang::Decl*) + 1874
16 libclang-cpp.10.dylib    0x000000010d9d46ca clang::Parser::ParseCXXMemberSpecification(clang::SourceLocation, clang::SourceLocation, clang::Parser::ParsedAttributesWithRange&, unsigned int, clang::Decl*) + 2378
17 libclang-cpp.10.dylib    0x000000010d9d1f7a clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::Parser::ParsedAttributesWithRange&) + 5402
18 libclang-cpp.10.dylib    0x000000010d9b0cb6 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*) + 1094
19 libclang-cpp.10.dylib    0x000000010d9d7644 clang::Parser::ParseCXXClassMemberDeclaration(clang::AccessSpecifier, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo const&, clang::ParsingDeclRAIIObject*) + 2244
20 libclang-cpp.10.dylib    0x000000010da4cc4b clang::Parser::ParseSingleDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo const&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) + 315
21 libclang-cpp.10.dylib    0x000000010da4c3a0 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) + 1344
22 libclang-cpp.10.dylib    0x000000010d9d6eac clang::Parser::ParseCXXClassMemberDeclaration(clang::AccessSpecifier, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo const&, clang::ParsingDeclRAIIObject*) + 300
23 libclang-cpp.10.dylib    0x000000010d9da152 clang::Parser::ParseCXXClassMemberDeclarationWithPragmas(clang::AccessSpecifier&, clang::Parser::ParsedAttributesWithRange&, clang::TypeSpecifierType, clang::Decl*) + 1874
24 libclang-cpp.10.dylib    0x000000010d9d46ca clang::Parser::ParseCXXMemberSpecification(clang::SourceLocation, clang::SourceLocation, clang::Parser::ParsedAttributesWithRange&, unsigned int, clang::Decl*) + 2378
25 libclang-cpp.10.dylib    0x000000010d9d1f7a clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::Parser::ParsedAttributesWithRange&) + 5402
26 libclang-cpp.10.dylib    0x000000010d9b0cb6 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo const&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*) + 1094
27 libclang-cpp.10.dylib    0x000000010da4ce71 clang::Parser::ParseSingleDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo const&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) + 865
28 libclang-cpp.10.dylib    0x000000010da4c3a0 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) + 1344
29 libclang-cpp.10.dylib    0x000000010da4bcbf clang::Parser::ParseDeclarationStartingWithTemplate(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) + 255
30 libclang-cpp.10.dylib    0x000000010d9b00f9 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&, clang::SourceLocation*) + 745
31 libclang-cpp.10.dylib    0x000000010da5ea05 clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) + 213
32 libclang-cpp.10.dylib    0x000000010d9cba39 clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) + 281
33 libclang-cpp.10.dylib    0x000000010d9cb568 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) + 5992
34 libclang-cpp.10.dylib    0x000000010d9b02a6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&, clang::SourceLocation*) + 1174
35 libclang-cpp.10.dylib    0x000000010da5ea05 clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) + 213
36 libclang-cpp.10.dylib    0x000000010d9cba39 clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) + 281
37 libclang-cpp.10.dylib    0x000000010d9cb568 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) + 5992
38 libclang-cpp.10.dylib    0x000000010d9b02a6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&, clang::SourceLocation*) + 1174
39 libclang-cpp.10.dylib    0x000000010da5ea05 clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) + 213
40 libclang-cpp.10.dylib    0x000000010d9cba39 clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) + 281
41 libclang-cpp.10.dylib    0x000000010d9cb568 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) + 5992
42 libclang-cpp.10.dylib    0x000000010d9b02a6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::Parser::ParsedAttributesWithRange&, clang::SourceLocation*) + 1174
43 libclang-cpp.10.dylib    0x000000010da5ea05 clang::Parser::ParseExternalDeclaration(clang::Parser::ParsedAttributesWithRange&, clang::ParsingDeclSpec*) + 213
44 libclang-cpp.10.dylib    0x000000010da5d53a clang::Parser::ParseTopLevelDecl(clang::OpaquePtr<clang::DeclGroupRef>&, bool) + 1066
45 libclang-cpp.10.dylib    0x000000010d99eeed clang::ParseAST(clang::Sema&, bool, bool) + 541
46 libclang-cpp.10.dylib    0x000000010f1cbeb8 clang::FrontendAction::Execute() + 168
47 libclang-cpp.10.dylib    0x000000010f15fdc1 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) + 1553
48 libclang-cpp.10.dylib    0x000000010f23f81e clang::ExecuteCompilerInvocation(clang::CompilerInstance*) + 2190
49 clang-10                 0x000000010adbce11 cc1_main(llvm::ArrayRef<char const*>, char const*, void*) + 2177
50 clang-10                 0x000000010adbacd6 ExecuteCC1Tool(llvm::SmallVectorImpl<char const*>&) + 358
51 libclang-cpp.10.dylib    0x000000010edf70a7 void llvm::function_ref<void ()>::callback_fn<clang::driver::CC1Command::Execute(llvm::ArrayRef<llvm::Optional<llvm::StringRef> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >*, bool*) const::$_1>(long) + 23
52 libLLVM-10.dylib         0x0000000114cbd36a llvm::CrashRecoveryContext::RunSafely(llvm::function_ref<void ()>) + 218
53 libclang-cpp.10.dylib    0x000000010edf6434 clang::driver::CC1Command::Execute(llvm::ArrayRef<llvm::Optional<llvm::StringRef> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >*, bool*) const + 404
54 libclang-cpp.10.dylib    0x000000010edc1021 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&) const + 433
55 libclang-cpp.10.dylib    0x000000010edc15dc clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*> >&) const + 140
56 libclang-cpp.10.dylib    0x000000010eddc7fc clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*> >&) + 444
57 clang-10                 0x000000010adba5ce main + 10590
58 dyld                     0x00007ff804adc310 start + 2432
clang-10: error: clang frontend command failed due to signal (use -v to see invocation)
clang version 10.0.0 
Target: x86_64-apple-darwin22.3.0
Thread model: posix
InstalledDir: /Users/molarinr/miniconda3/envs/res/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).

The problem seems to be that the include for the the headers is broken somehow. I am running this within a conda environment.

Additional information:
OS: macOS 13.2.1

Python version: 3.9

Pystan version: 3.6.0

Compiler:
(Conda install)
clang version 10.0.0
Target: x86_64-apple-darwin22.3.0
Thread model: posix
InstalledDir: /Users/molarinr/miniconda3/envs/res/bin

Compiler:
(System install)
Apple clang version 14.0.0 (clang-1400.0.29.202)
Target: x86_64-apple-darwin22.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Any help with this is greatly appreciated. Thanks!

2

Using pip to install pystan from PyPI is the supported method of installing pystan. PyPI has precompiled wheels for your macOS system (x86-64). conda isn’t supported at this time.