numpy undefined symbol: PyFPE_jbuf

Question

I am trying to use the One Million Song Dataset, for this i had to install python tables, numpy, cython, hdf5, numexpr, and so.

Yesterday i managed to install all i needed, and after having some troubles with hdf5, i downloaded the precompiled binary packages and saved them in my /bin folder, and the respective libraries in /lib , after that i tested this python script : http://labrosa.ee.columbia.edu/millionsong/sites/default/files/tutorial1.py.txt

and it worked fine, to be clear the way i made it work was to first run the script and start installing the needed dependencies, but today i restarted my laptop and it didn't work, now it throws me this error on the console :

python2.7 script.py  

returns :

import numpy as np # get it at: http://numpy.scipy.org/ from . import random from .mtrand import * ImportError: /home/francisco/.local/lib/python2.7/site-packages/numpy/random/mtrand.so: undefined symbol: PyFPE_jbuf 

seems to me that there is a missing variable in such file, my guess is that the script is looking for the numpy library in the wrong place, since i made so many failed installations maybe i broke something and it only worked out because it was loaded in the temporal memory of the computer.

I tried installing Anaconda, and i created a new environment and installed the packaged with the anaconda package manager, and even thought i listed all packaged and it returns :

# packages in environment at /home/francisco/anaconda2/envs/Music: # biopython                 1.66                np110py27_0   cython                    0.23.4                    <pip> hdf5                      1.8.15.1                      2   mkl                       11.3.1                        0   numexpr                   2.5                 np110py27_0   numpy                     1.10.4                   py27_1   openssl                   1.0.2g                        0   pillow                    3.1.1                     <pip> pip                       8.1.1                    py27_0   pytables                  3.2.2               np110py27_1   python                    2.7.11                        0   python-ldap               2.4.25                    <pip> readline                  6.2                           2   reportlab                 3.3.0                     <pip> requirements              0.1                       <pip> setuptools                20.3                     py27_0   sqlite                    3.9.2                         0   tables                    3.2.2                     <pip> tk                        8.5.18                        0   wheel                     0.29.0                   py27_0   zlib                      1.2.8                         0   

i still get the same error. I really need help and don't know what else to try. Thanks.

Answer 1

I had the same problem, probably you have installed numpy without Anaconda, so there is a conflict because of this, which numpy to use: that one installed with pip or with conda. When I removed non-Anaconda numpy, error gone.

pip uninstall numpy