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jyyulab / SJARACNe

Scalable Tool for Gene Network Reverse Engineering
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problem to run sjaracne #24

Closed ERIGR closed 4 years ago

ERIGR commented 4 years ago

Hi,

I'm bioinformatician at the Gustave Roussy Institue in france and I want to try building new networks with SJ-ARACNE. To install J-ARACNE, I followed the method used in your readme file. So I install a conda environment called py36. Then I install numpy, scipy, pandas and cwltool using the requirements.txt file. I used the command pip install SJARACNe to install SJARACNe. Then, trying to use SJARACNE, I got the following error message : Traceback (most recent call last): File "/home/esteve/anaconda2/envs/py36/bin/sjaracne", line 11, in load_entry_point('SJARACNe==0.2.0', 'console_scripts', 'sjaracne')() File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/pkg_resources/init.py", line 490, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/pkg_resources/init.py", line 2855, in load_entry_point return ep.load() File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/pkg_resources/init.py", line 2446, in load return self.resolve() File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/pkg_resources/init.py", line 2452, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/init.py", line 1, in from .bin import File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/bin/init.py", line 2, in from .create_consensus_network import File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/bin/create_consensus_network.py", line 11, in from scipy import stats File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/scipy-1.0.1-py3.6-linux-x86_64.egg/scipy/stats/init.py", line 345, in from .morestats import * File "/home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/scipy-1.0.1-py3.6-linux-x86_64.egg/scipy/stats/morestats.py", line 12, in from numpy.testing.decorators import setastest ModuleNotFoundError: No module named 'numpy.testing.decorators'

What could be the problem ? Thank you.

adamdingliang commented 4 years ago

numpy.testing.decorators is deprecated since numpy 1.15.0. See the following post: https://github.com/numpy/numpy/issues/12599

While we are working on resolving this for the future versions of numpy, installing an older version (specified in the requirements.txt file) is recommended.