Compilation error in Pystan (macOS Mojave)

Interfaces PyStan
1

I’m trying to get pystan (2.18) working under Mojave and have found myself with the following dilemma. If I try to use the macOS gcc I get the following:

warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
/var/folders/rn/5cyhvg_x591146y8khk9vqz40000gp/T/tmp8ku2bvdo/stanfit4logistic_regression_b34cbd6e4c4687ee64f335b5b2408384_7347898005404304860.cpp:675:10: fatal error: 'ios' file not found
#include "ios"
         ^~~~~
1 warning and 1 error generated.

I’ve run xcode-select --install. Here’s the gcc version info:

$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

If I use gcc (GCC 4.8.5) installed with Anaconda 3 (5.3.0), I get

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /Users/jhuggins/anaconda3/envs/stan/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0,
                 from /Users/jhuggins/anaconda3/envs/stan/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34,
                 from /Users/jhuggins/anaconda3/envs/stan/include/python3.6m/Python.h:11,
                 from /var/folders/rn/5cyhvg_x591146y8khk9vqz40000gp/T/tmp33mvc0fh/stanfit4logistic_regression_b34cbd6e4c4687ee64f335b5b2408384_8158677822526299729.cpp:57:
/Users/jhuggins/anaconda3/envs/stan/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory
 #include_next <limits.h>  /* recurse down to the real one */
                                                             ^
2

Open up Spotlight and find where the limits.h file lives. Then, you are going have to add that directory to the search path for system headers.

3

Hi,

First, use pip version pip install pystan and try compiling again.

There seems to be similar problems with mojave


Run this (in pandas issue) and try again:

/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

If that doesn’t work, then remove xcode and commandline tools and do the fresh install.

Run all these tests in fresh conda-env.

Install PyStan from source to a new conda env.

conda create -n stan_env python=3.7 numpy cython
conda activate stan_env

Then install from source (needs git, install with conda if not found; conda install git)

pip install git+https://github.com/stan-dev/pystan
1 Like
4

Thank you, ahartikainen! Your posts here and on GitHub are the only reason I fixed this bug in my own build. Running macOS_SDK_headers_for_macOS_10.14.pkg was all that was required.

1 Like