CODEWITHSUNDEEP
pythonanacondapymc
Javier
Javier

Reputation: 1550

Error when importing PyMC

I have just installed PyMC on my mac (10.9.4) using anaconda (Anaconda 2.0.1) and the following command I copied from the pymc distribution page:

conda install -c https://conda.binstar.org/pymc pymc

Everything seemed to be alright during the installation (no error messages, all the fetching completed). Then when I imported it I got the following error messages: 

>>> import pymc
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/anaconda/lib/python2.7/site-packages/pymc/__init__.py", line 30, in <module>
    from .CommonDeterministics import *
  File "/anaconda/lib/python2.7/site-packages/pymc/CommonDeterministics.py", line 21 in <module>
    from .utils import safe_len, stukel_logit, stukel_invlogit, logit, invlogit, value, find_element
  File "/anaconda/lib/python2.7/site-packages/pymc/utils.py", line 14, in <module>
from . import flib
ImportError: dlopen(/anaconda/lib/python2.7/site-packages/pymc/flib.so, 2): Library not loaded: /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.3.dylib
  Referenced from: /anaconda/lib/python2.7/site-packages/pymc/flib.so
  Reason: image not found

I am new to python and I don't really know what to do next to not mess up. I typed this to find other packages:

 binstar search -t conda pymc

 Packages:
                      Name | Access       | Package Types   | Summary             
 ------------------------- | ------------ | --------------- | --------------------
             asmeurer/pymc | public       | conda           | https://github.com/pymc-devs/pymc
                auto/pymcu | published    | conda           | http://www.pymcu.com
             bkreider/pymc | public       | conda           | https://github.com/pymc-devs/pymc
      datamicroscopes/pymc | public       | conda           | None                
           fonnesbeck/pymc | public       | conda           | https://github.com/pymc-devs/pymc
             jonsedar/pymc | public       | conda           | None                
                 pymc/pymc | public       | conda           | None                
             rsignell/pymc | public       | conda           | Markov Chain Monte Carlo sampling toolkit.
          tobeplugged/pymc | public       | conda           | None                
           tomku-test/pymc | published    | conda           | https://github.com/pymc-devs/pymc

so, should I just try to reinstall pymc using one of these packages, and if so, is the command the following?: 

 conda install -c https://github.com/pymc-devs/pymc pymc

should I remove 1st the package previously installed? or the new installation will over-write(?). Or perhaps it is easy to fix those errors I found before?

Thanks

Upvotes: 1

Views: 3250

Answers (3)

Paul
Paul

Reputation: 4168

gfortran now seems to be part of gcc

NOTE: the below takes a while, took me 80 minutes to install this on MacBook pro
brew install gcc

BTW, the above also seems to be a required installation if you want to use PyMC and are not using the anaconda distribution

Upvotes: 2

asmeurer
asmeurer

Reputation: 91680

Another way that should work (on Mac OS X) is to conda install -c asmeurer pymc. This will install the gcc package (which includes gfortran) from my Binstar channel along with pymc.

Upvotes: 1

elyase
elyase

Reputation: 41003

You are missing gfortran. If you haven't first install brew:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Follow the instructions and once brew is correctly set up just do:

brew install gfortran

Upvotes: 1

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