2

This is a PyStan model that I am trying to run. However, once I try to run it I come across the following error:

CompileError: command 'gcc' failed with exit status 1

Any idea how this error could be fixed on the macOS?

counts = [0.0711, 0.125, 0.0121, 0.00513, 0.112, 0.0694, 0.0166, 0.163, 0.0481, 0.0762, 0.175, 0.117, 0.211, 0.0468, 0.0272, 0.134, 0.035, 0.0125, 0.0834, 0.011, 0.0226, 0.0652, 0.132, 0.0738, 0.206, 0.107, 0.0354, 0.0853, 0.0219, 0.106, 0.165, 0.0729, 0.111, 0.0352, 0.0749, 0.00188, 0.00146, 0.0113, 0.0175, 0.167, 0.0736, 0.00292, 0.0378, 0.116, 0.145, 0.161, 0.292, 0.0158, 0.207, 0.481, 0.066, 0.0926, 0.0188, 0.103, 0.262, 0.167, 0.163, 0.0357, 0.137, 0.0699, 0.00632, 0.012, 0.124, 0.159, 0.000179, 0.0441, 0.16, 0.196, 0.131, 0.0731, 0.0282, 0.046, 0.089, 0.0318, 0.0303, 0.0269, 0.184, 0.144, 0.0981, 0.277, 0.0277, 0.000416, 0.225, 0.0538, 0.0422, 0.186, 0.00116, 0.0118, 0.0668, 0.157, 0.12, 0.0285, 0.0204, 0.0702, 0.0692, 0.126, 0.00857, 0.0322, 0.029, 0.0737, 0.0811, 0.0172, 0.121, 0.0589, 0.00973, 0.0797, 0.0996, 0.0862, 0.185, 0.0671, 0.0142, 0.0669, 0.0739, 0.12, 0.566, 0.0179, 0.0483, 0.0382, 0.0109, 0.058, 0.0252, 0.0368, 0.0241, 0.156, 0.0696, 0.015, 0.0759, 0.0431, 0.0798, 0.0816, 0.108, 0.0155, 0.0211, 0.00171, 0.00148, 0.0117, 0.0164, 0.0681, 0.000238, 0.00691, 0.127, 0.0502, 0.00598, 0.0722, 0.0174, 0.0627, 0.00372, 0.0648, 0.0343, 0.101, 0.0751, 0.0111, 0.189, 0.0298, 0.0563, 0.0123, 0.00126, 0.0407, 0.0203, 0.143, 0.0488, 0.0696, 0.0145, 0.0474, 0.0245, 0.172, 0.17, 0.109, 0.182, 0.0357, 0.0729, 0.295, 0.041, 0.207, 0.0725, 0.107, 0.00257, 0.0252, 0.0866, 0.00576, 0.0468, 0.13, 0.0881, 0.115, 0.0321, 0.000605, 0.0392, 0.017, 0.0408, 0.00253, 0.132, 0.298, 0.109, 0.00814, 0.0338, 0.0253, 0.0153, 0.0475, 0.0624, 0.199, 0.265, 0.0202, 0.199, 0.135, 0.0285, 0.0728, 0.124, 0.0165, 0.0385, 0.0843, 0.0988, 0.139, 0.0311, 0.0837, 0.0931, 0.182, 0.0129, 0.00582, 0.0166, 0.109, 0.039, 0.0892, 0.0269, 0.0407, 0.154, 0.109, 0.212, 0.112, 0.0252, 0.00368, 0.0556, 0.103, 0.0754, 0.0135, 0.106, 0.184, 0.0462, 0.0152, 0.0438, 0.105, 0.0283, 0.0417, 0.229, 0.103, 0.0628, 0.0499, 0.122, 0.0227, 0.0451, 0.164, 0.121, 0.0665, 0.00797, 0.113, 0.0421, 0.166, 0.062, 0.129, 0.0966, 0.0167, 0.211, 0.0155, 0.129, 0.0595, 0.0219, 0.105, 0.0483, 0.0959, 0.064, 0.00275, 0.166, 0.0134, 0.0549, 0.235, 0.06, 0.000117, 0.00322, 0.0557, 0.0555, 0.169, 0.211, 0.0521, 0.0485, 0.0173, 0.0644, 0.109, 0.043, 0.0111, 0.215, 0.114, 0.0552, 0.00457, 0.219, 0.314, 0.049, 0.0113, 0.0513, 0.151, 0.00505, 0.0232, 0.0637, 0.0347, 0.0247, 0.000251, 0.0439, 0.00442, 0.124, 0.115, 0.0601, 0.209, 0.422, 0.0646, 0.00895, 0.047, 0.125, 0.0196, 0.187, 0.0125, 0.00415, 0.0394, 0.035, 0.046, 0.0236, 0.0551, 0.152, 0.0371, 0.00205, 0.0499, 0.0565, 0.0341, 0.0509, 0.0589, 0.0456, 0.0365, 0.00266, 0.0681, 0.0565, 0.0045, 0.0144, 0.0601, 0.0303, 0.0349, 0.0441, 0.0328, 0.0733, 0.0488, 0.0717, 0.269, 0.0997, 0.0157, 0.00706, 0.0426, 0.149, 0.0473, 0.0846, 0.0519, 0.0223, 0.0848, 0.0145, 0.00368, 5.87e-05, 0.0163, 0.0841, 0.171, 0.0538, 0.0445, 0.147, 0.0236, 0.115, 0.193, 0.00451, 0.014, 0.0687, 0.00123, 0.13, 0.0513, 0.0662, 0.15, 0.133, 0.0459, 0.0777, 0.0442, 0.106, 0.0114, 0.00198, 0.00188, 0.105, 0.155, 0.098, 0.0762, 0.12, 0.00772, 0.0203, 0.0309, 0.0198, 0.0654, 0.106, 0.0853, 0.000944, 0.000954, 0.109, 0.0293, 0.0693, 0.0262, 0.0767, 0.307, 0.0163, 0.0962, 0.0224, 0.00329, 0.00259, 0.0164, 0.0481, 0.194, 0.00661, 0.111, 0.00302, 0.154, 0.00364, 0.0176, 0.0554, 0.0916, 0.0313, 0.0198, 0.121, 0.145, 0.0539, 0.101, 0.127, 0.0408, 0.0882, 0.0538, 0.0717, 0.104, 0.113, 0.00819, 0.146, 0.000258, 0.0787, 0.115, 0.0136, 0.0367, 0.0852, 0.0565, 0.0666, 0.105, 0.0834, 0.0789, 0.0496, 0.0952, 0.0742, 0.0143, 0.0627, 0.0164, 0.079, 0.021, 0.0803, 0.000524, 0.0245, 0.0097, 0.0599, 0.0469, 0.0176, 0.0708, 0.0731, 0.0614, 0.085, 0.0221, 0.191, 0.00177, 0.0272, 0.0567, 0.0255, 0.00566, 0.122, 0.15, 0.0715, 0.0338, 0.0193, 0.00552, 0.0457, 0.208, 0.174, 0.0026, 0.0656, 0.0742, 0.022, 0.0382, 0.172, 0.0209, 0.04, 0.117, 0.0217, 0.000618, 0.0459, 0.00841, 0.0104, 0.0509, 0.104, 0.000327, 0.0042, 0.0902, 0.0341, 0.091, 0.0569, 0.027, 0.184, 0.0343, 0.19, 0.00992, 0.111, 0.225, 0.0608, 0.0927, 0.0617, 0.0808, 0.00346, 0.161, 0.055, 0.105, 0.506, 0.0304, 0.0163, 0.0973, 0.000753, 0.0564, 0.0032, 0.00947, 0.0337, 0.0905, 0.0918, 0.0315, 0.0155, 0.0425, 0.00194, 0.00797, 0.103, 0.000849, 0.00948, 0.0641, 0.0765, 0.0982, 0.00755, 0.0969, 0.0585, 0.102, 0.012, 0.0807, 0.181, 0.255, 0.0239, 0.00207, 0.00591, 0.0988, 0.0383, 0.204, 0.0168, 0.0487, 0.0326, 0.0457, 0.0212, 0.0192, 0.185, 0.0876, 0.00121, 0.0229, 0.023, 0.0986, 0.0831, 0.0192, 0.142, 0.00611, 0.0369, 0.0496, 0.0523, 0.0471, 0.0315, 0.0202, 0.0342, 0.00263, 0.307, 0.0354, 0.0234, 0.133, 0.124, 0.0744, 0.114, 0.102, 0.0694, 0.0626, 0.0245, 0.00579, 0.124, 0.171, 0.212, 0.0113, 0.00475, 0.00489, 0.0727, 0.0388, 0.0584, 0.207, 0.0665, 0.143, 0.0714, 0.192, 0.197, 0.053, 0.0309, 0.0151, 0.0495, 0.0143, 0.0837, 0.138, 0.00898, 0.195, 0.0225, 0.0251, 0.0159, 0.121, 0.0887, 0.0277, 0.0282, 0.162, 0.018, 0.28, 0.00839, 0.0286, 0.0063, 0.0313, 0.021, 0.0609, 0.00187, 0.00668, 0.0366, 0.0598, 0.0707, 0.174, 0.109, 0.0608, 0.0313, 0.109, 0.0132, 0.087, 0.00677, 0.018, 0.044, 0.017, 0.158, 0.0442, 0.114, 0.0673, 0.0326, 0.031, 0.0724, 0.14, 0.0186, 0.00151, 0.0302, 0.0386, 0.201, 0.00411, 0.00878, 0.0313, 0.000188, 0.0748, 0.0779, 0.00582, 0.07, 0.0113, 0.00965, 0.151, 0.0443, 0.011, 0.0381, 0.00801, 0.0203, 0.164, 0.0242, 0.0217, 0.0261, 0.0627, 0.000245, 0.0106, 0.00567, 0.0736, 0.02, 0.0391, 0.0105, 0.0925, 0.00756, 0.0102, 0.013, 0.00146, 0.088, 0.0247, 0.063, 0.00596, 0.0107, 0.0358, 0.013, 0.0117, 0.0256, 0.0265, 0.368, 0.00302, 0.00357, 0.0419, 0.0245, 0.0563, 0.109, 0.0796, 0.109, 0.0567, 0.0207, 0.00938, 0.256, 0.0557, 0.113, 0.011, 0.00809, 0.0214, 0.00244, 0.0161, 0.0297, 0.128, 0.0223, 0.0113, 0.0275, 0.0196, 0.0121, 0.0773, 0.0428, 0.0674, 0.0116, 0.0186, 0.129, 0.146, 0.0766, 0.000269, 0.0149, 0.0493, 0.00883, 0.00656, 0.00548, 0.0193, 0.00948, 0.0633, 0.0361, 0.0742, 0.0427, 0.0274, 0.0539, 0.027, 0.0145, 0.0388, 0.0271, 0.0036, 0.0812, 0.0378, 0.0195, 0.0164, 0.0615, 0.101, 0.0605, 0.0494, 0.0609, 0.0538, 0.0205, 0.0187, 0.0147, 0.00858, 0.0905, 0.196, 0.0792, 0.0445, 0.0575, 0.0126, 0.173, 0.0379, 0.104, 0.0854, 0.0465, 0.145, 0.00447, 0.0506, 0.0499, 0.0213, 0.0521, 0.0466, 0.0131, 0.0197, 0.0454, 0.00161, 0.0168, 0.00849, 0.0663, 0.0081, 0.00594, 0.0428, 0.0157, 0.102, 0.0309, 0.0543, 0.0236, 0.0154, 0.0214, 0.106, 0.00881, 0.226, 0.0497, 0.0386, 0.0864, 0.0155, 0.139, 0.116, 0.0409, 0.0534, 0.0877, 0.022, 0.0179, 0.0112, 0.0302, 0.0123, 0.11, 7.21e-06, 0.111, 0.0548, 0.127, 0.00477, 0.13, 0.00288, 0.0602, 0.147, 0.0207, 0.132, 0.00212, 0.0246, 0.0776, 0.0598, 0.114, 0.0272, 0.0079, 0.0285, 0.0111, 0.103, 0.296, 0.0313, 0.0384, 0.00446, 0.0657, 0.0114, 0.342, 0.0434, 0.0266, 0.109, 0.00581, 0.0155, 0.0322, 0.046, 0.0816, 0.056, 0.0124, 0.0329, 0.126, 0.0381, 0.0393, 0.0154, 0.00345, 0.00226, 0.114, 0.0881, 0.00316, 0.0388, 0.111, 0.0139, 0.0205, 0.0119, 0.0705, 0.0219, 0.0765, 0.0729, 0.0485, 0.00661, 0.169, 0.00679, 0.0538, 0.00537, 0.01, 0.047, 0.0325, 0.0668]



stan_code = """

 data {
   int<lower=1> C;    // number of calls in 11th
   real<lower=0> alpha;   // prior hyperparameters for gamma
   real<lower=0> beta;   // prior hyperparameters for gamma
   real<lower=0> counts[C];   
}

parameters {
    real<lower=0> lambda; 
}


model {
   lambda ~ gamma(alpha,beta);
   counts ~ exponential(lambda);   
   }
"""

stan_model = pystan.StanModel(model_code=stan_code)

stan_data = {
   'C': 892,
   'alpha': [0.5],
   'beta': [0.5],
   'counts': counts,
}

results = stan_model.sampling(data=stan_data)

print(results)
Ewa Szyszka
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5 Answers5

1

I experienced a similar problem. I solved it using conda. Suppose you've created a conda environment called pystan. Activate it, and then install gcc:

    $ source activate pystan
(pystan)$ conda install gcc

Then make sure you install pystan's dependencies, and pip-install pystan

(pystan)$ pip install pystan

These steps solve the problem in my case, I hope it helps.

Shaido
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Sergio Rossell
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1

gcc -v showed that my gcc version is 4.2.x, and Stan 2.19.0.0 requires gcc 4.9.3 or higher. So I installed gcc49 using Homebrew:

$ brew install gcc49

If gcc -v still doesn't print 4.9.x, but gcc-4.9 -v does, then you should create a link to the gcc and g++ executables you just installed:

$ sudo ln -s `which gcc-4.9` /usr/local/bin/gcc
$ sudo ln -s `which g++-4.9` /usr/local/bin/g++

The following step is probably not needed, but as explained here, on reasonably new macOS and Xcode you should also execute the following installer (at least if you use the compiler that comes with Xcode which we don't):

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

I use PyStan in a Conda environment, installed as such:

$ conda create -n pystan python=3.7
$ conda activate pystan
(pystan) $ pip install pystan

The order of the above steps might matter.

Laszlo Treszkai
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  • For me the linking doesn't work, when I call gcc -v it always uses the xcode c++ version (which is 4.2.1) – Deproblemify Nov 22 '19 at 11:55
  • To be more precise even though the linking is successful, when I run `gcc -v` I do not get the same output as `gcc-4.9 -v` – Deproblemify Nov 22 '19 at 12:04
  • Also I have been using `conda` which seems to use an own version of clang so it is important to install `pystan` using the `conda-forge` channel and not using `pip`! Hope this helps others in the future (I know this question was specifically *not* about `conda`). – Deproblemify Nov 23 '19 at 14:56
1

For anyone (like me) very lost and finding their way here, this is what worked for me...

System:

OS: macOS Big Sur v11.3
pystan.__version__ '2.19.1.1'
Python 3.8.8

Problem

I was getting a CompileError when running:

import pystan
model_code = 'parameters {real y;} model {y ~ normal(0,1);}'
model = pystan.StanModel(model_code=model_code)  # this will take a minute
y = model.sampling(n_jobs=1).extract()['y']
y.mean()  # should be close to 0

Solution

  1. Ensure gcc & xcode version installed & up-to-date (brew install gcc && xcode-select --install)
  2. As per this thread check gcc and g++ version by running ls /usr/local/bin | grep gcc and ls /usr/local/bin | grep g++ and add these as env variables. In my case I added these lines to my ~/.bash_profile:
# for c++ libraries - reqiured for pystan / prophet
export CC=gcc-11
export CXX=g++-11
Tommy Neeld
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0

I hope this would be helpful for others, what worked at the end for me was to install python3 and run this code in terminal

source activate py36 jupyter notebook

Ewa Szyszka
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0
sudo xcode-select --reset

If you are using Mac M1 and due to some files corrupt or delete, you get this issue while you have gcc installed you can use this and then run the installation of the package.

My case it was detectron2 in a new env

gamingflexer
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