search

applied-bioinformatics / An-Introduction-To-Applied-Bioinformatics

Interactive lessons in bioinformatics.
http://readIAB.org
Other
805 stars 316 forks source link

ImportError: cannot import name '_hierarchy' #178

Closed jg44 closed 9 years ago

jg44 commented 9 years ago

Hello,

I recently (re)installed IAB using the following command:

conda create --name iab -c http://conda.binstar.org/gregcaporaso python=3.4 iab

(See: https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/blob/master/book/getting-started/reading-iab.md#installation-)

I had earlier issues linked to this issue: https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/issues/165#issuecomment-125396536

but I thought they were solved.

Now I'm getting the following message about importing "heirarchy" when running the IAB notebook which I gather are again linked to the scipy installation. See below. I am on a Mac, OS 10.9.

Any thoughts? Thanks,

Jeff

from iab.algorithms import format_matrix

ImportError Traceback (most recent call last)

in () ----> 1 from iab.algorithms import format_matrix /Users/jeff/miniconda3/lib/python3.4/site-packages/iab/algorithms/**init**.py in () 11 12 import numpy as np ---> 13 from scipy.cluster.hierarchy import average, dendrogram, to_tree 14 from skbio.sequence import BiologicalSequence 15 from skbio.stats.distance import DistanceMatrix /Users/jeff/miniconda3/lib/python3.4/site-packages/scipy/cluster/**init**.py in () 25 **all** = ['vq', 'hierarchy'] 26 ---> 27 from . import vq, hierarchy 28 29 from numpy.testing import Tester /Users/jeff/miniconda3/lib/python3.4/site-packages/scipy/cluster/hierarchy.py in () 173 174 import numpy as np --> 175 from . import _hierarchy 176 import scipy.spatial.distance as distance 177 ImportError: cannot import name '_hierarchy'
gregcaporaso commented 9 years ago

@jg44, sorry for the slow reply. I don't have the conda install working yet (it's in progress in #167). This will be the primary means of installation for 0.1.2, which will be released in December, 2015. For now, the best way to install is to follow the install notes in the release version of the Getting Started chapter. Sorry for the trouble!

jg44 commented 9 years ago

Thanks. I just can't get things working properly using the pip install. Major problems with scipy on both Mac and Ubuntu. I will just wait for the conda-based release. Thanks for your response.

gregcaporaso commented 9 years ago

You should be able to conda install scipy, and then pip install IAB (pip works within conda).

On Mon, Nov 9, 2015 at 4:32 PM, jg44 notifications@github.com wrote:

Thanks. I just can't get things working properly using the pip install. Major problems with scipy on both Mac and Ubuntu. I will just wait for the conda-based release. Thanks for your response.

— Reply to this email directly or view it on GitHub https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/issues/178#issuecomment-155232681 .