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ImportError when using rpy2 with numpy.testing

While doing unit testing with the numpy.testing module, I ran into a rather strange error. I am running iPython notebook in a virtual machine. In my code, I have one test where I compare my output to the data in R. This requires me to load the rpy2 modules like this:

import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
fastclime = importr('fastclime')
grdevices = importr('grDevices')

However, when I run ! py.test

I get the following error:

=============================== ERRORS ==================== =================

_____________________ ERROR collecting test_fastclime_R.py _____________________
test_fastclime_R.py:6: in <module>
    import rpy2.robjects as robjects
../../anaconda/lib/python2.7/site-packages/rpy2/robjects/__init__.py:15: in <module>
    import rpy2.rinterface as rinterface
../../anaconda/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:101: in <module>
    from rpy2.rinterface._rinterface import *
E   ImportError: /home/bitnami/anaconda/bin/../lib/libreadline.so.6: undefined symbol: PC
====================== 10 passed, 1 error in 0.19 seconds ======================

I suspect this is because some environment variable is not associated with my working directory, but I have no idea how to fix it. Any suggestions are greatly appreciated! Thank!

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2 answers


The solution was

1) delete the directory __pycache__

if a previous version was created



2) Install readline in anaconda on the command line: conda install -c asmeurer readline

3) Inside the .py file there is import readline

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another solution is to remove conda readline from the environment and use pip one:



conda remove --force readline
pip install readline
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