Command 'gcc' failed with exit status 1

[idumahg]

Summary:

Hi, I am new to pystan, an error occurs when I compile a model. It gives two kinds of error. I have tried looking at other threads that addressed this, but all the recommendations I have tried hasn't worked:

distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1 distutils.errors.CompileError: command 'gcc' failed with exit status 1

Description:

I am running this in a Python 3 environment.

Reproducible Steps:

import pystan schools_code = """ data { int J; // number of schools real y[J]; // estimated treatment effects real sigma[J]; // s.e. of effect estimates } parameters { real mu; real tau; real eta[J]; } transformed parameters { real theta[J]; for (j in 1:J) theta[j] = mu + tau * eta[j]; } model { eta ~ normal(0, 1); y ~ normal(theta, sigma); } """

schools_dat = {'J': 8, 'y': [28, 8, -3, 7, -1, 1, 18, 12], 'sigma': [15, 10, 16, 11, 9, 11, 10, 18]}

sm = pystan.StanModel(model_code=schools_code) fit = sm.sampling(data=schools_dat, iter=1000, chains=4)

print(fit)

eta = fit.extract(permuted=True)['eta'] np.mean(eta, axis=0)

Current Output:

The current output. Knowing what is the current behavior is useful. INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_0fe254f3c524d4153537de9712f3f235 NOW. Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py", line 118, in _compile extra_postargs) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py", line 909, in spawn spawn(cmd, dry_run=self.dry_run) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py", line 36, in spawn _spawn_posix(cmd, search_path, dry_run=dry_run) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py", line 159, in _spawn_posix % (cmd, exit_status)) distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Users/gideonidumah/Desktop/Internship/msgi_2020_gideon/hodgkinhuxley_inversion/Stan.py", line 29, in sm = pystan.StanModel(model_code=schools_code) File "/Users/gideonidumah/Desktop/Internship/msgi_2020_gideon/sir_inversion_python/env/lib/python3.7/site-packages/pystan/model.py", line 378, in init build_extension.run() File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 340, in run self.build_extensions() File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions self._build_extensions_serial() File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial self.build_extension(ext) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension depends=ext.depends) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py", line 574, in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py", line 120, in _compile raise CompileError(msg) distutils.errors.CompileError: command 'gcc' failed with exit status 1

Process finished with exit code 1

Expected Output:

Describe what you expect the output to be. Knowing the correct behavior is also very useful.

PyStan Version:

Python Version:

Operating System:

Mac OS Catalina Version 10.15.5