ImportError: libgfortran.3.dylib

[balzer82]

I am working on MacOS Mavericks and made

sudo port install py27-numpy py27-scipy py27-matplotlib py27-ipython +notebook py27-pandas py27-sympy py27-nose
--->  Computing dependencies for py27-numpy
--->  Cleaning py27-numpy
--->  Computing dependencies for py27-scipy
--->  Cleaning py27-scipy
--->  Computing dependencies for py27-matplotlib
--->  Cleaning py27-matplotlib
--->  Computing dependencies for py27-ipython
--->  Cleaning py27-ipython
--->  Computing dependencies for py27-pandas
--->  Cleaning py27-pandas
--->  Computing dependencies for py27-sympy
--->  Cleaning py27-sympy
--->  Computing dependencies for py27-nose
--->  Cleaning py27-nose
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.

And I installed GFortran, which is located in /usr/local/gfortran/.

But when I try to

python
Python 2.7.6 (default, Apr  9 2014, 11:48:52) 
[GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.interpolate
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/scipy/interpolate/__init__.py", line 160, in <module>
    from .interpolate import *
  File "/Library/Python/2.7/site-packages/scipy/interpolate/interpolate.py", line 15, in <module>
    import scipy.special as spec
  File "/Library/Python/2.7/site-packages/scipy/special/__init__.py", line 546, in <module>
    from ._ufuncs import *
ImportError: dlopen(/Library/Python/2.7/site-packages/scipy/special/_ufuncs.so, 2): Library not loaded: /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.3.dylib
  Referenced from: /Library/Python/2.7/site-packages/scipy/special/_ufuncs.so
  Reason: image not found

[pv]

This does not seem like a bug on our side, but more like a compiler installation issue, so closing the ticket. You can try asking on stackoverflow or mailing lists.

[matthew-brett]

Are you sure that python is picking up the macports python there?

Does macports really install its scipy into /Library/Python/2.7/site-packages/scipy ?

[balzer82]

You guys are completely right!! I forced to rebuild everything, now it works:

sudo pip install --upgrade --force-reinstall numpy
sudo pip install --upgrade --force-reinstall scipy

👍

[exowanderer]

3+ years later ... same problem ... same solution!

Thank you all -- especially @balzer82 for coming back and giving us the solution after you found it!

[Rachine]

Matlab runtime was messing around some of my python libs:

• had to remove Matlab runtime totally from my mac
• had to rebuild everything also

[HairuiLiu]

helped so much ~~ though i still wonder why reinstall numpy and scipy worked

[Ido-PX]

2019 and the same tip helped. Thanks @balzer82

[pmaji]

This still works as a solution! Had this problem recently with the pyjanitor package and this fixed it right away (after trying many other solutions). Link to the notebook that it had broken below, for context. Thank you @balzer82 for this!

https://github.com/pmaji/data-science-toolkit/blob/master/eda-and-visualization/radar_charts.ipynb