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Weird Numpy Error When I Try To Install Weblogo 3... Any Ideas?

python setup.py

Traceback (most recent call last): File "setup.py", line 20, in <module> from weblogolib import __version__ File "/home/margaret/Programs/weblogo-3.3/weblogolib/__init__.py", line 108, in <module> from numpy import array, asarray, float64, ones, zeros, int32,all,any, shape File "/usr/local/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module> from . import add_newdocs File "/usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 18, in <module> from .polynomial import * File "/usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 19, in <module> from numpy.linalg import eigvals, lstsq, inv File "/usr/local/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line 50, in <module> from .linalg import * File "/usr/local/lib/python2.7/dist-packages/numpy/linalg/linalg.py", line 29, in <module> from numpy.linalg import lapack_lite, _umath_linalg ImportError: /usr/local/lib/python2.7/dist-packages/numpy/linalg/lapack_lite.so: undefined symbol: ATL_dptsyrk

Any ideas of what's causing this error? Looks like some kind of numpy issue and probably not anything to do with Weblogo. Here is the link to Weblogo just in case (http://weblogo.threeplusone.com/)

Would appreciate any advice you can give :)

python
• 8,501 views • link
written by margiezilla margiezilla

It looks like python was compiled to use ATLAS with pthread support. You may find this thread from the scipy list helpful.

• 292 views • link
written by Devon Ryan Devon Ryan

Thanks, but their suggestions didn't work either....

• 0 views • link
written by margiezilla margiezilla

1 answer

I figured it out! I remembered that I had install numpy like so

sudo apt-get install python-numpy

so I first did:
sudo apt-get remove python-numpy
sudo apt-get autoremove

but then going into python and checking to make sure numpy was not there, I tried

import numpy

and it gave me the same error with /usr/local/lib/python2.7/dist-packages/numpy/linalg/lapack_lite.so:

So I went into /usr/local/lib/python2.7/dist-packages/

and I sudo rm -r the numpy folder as well as the numpy egg

and then I checked python again with import numpy and it finally showed that numpy had been removed

then I reinstalled with sudo apt-get install python-numpy

import numpy then works in python! (no errors).

So I went back into weblogo directory and did:

python setup.py build
python test_weblogo.py
sudo python setup.py install

and it compiled and installed just fine!

• 444 views • link
written by margiezilla margiezilla

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