search

phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
118 stars 31 forks source link

conda installation error #94

Closed Anto007 closed 2 years ago

Anto007 commented 2 years ago

Hi,

I found the below error when attempting installation via conda. The error doesn't go away even when I include mob_suite==3.0.0 and pandas==1.0.5 in my .yml file. Any help here would be appreciated. My .yml file looks like the below name: null

channels:

dependencies:

Below are the command-line and error messages I got. conda env create --prefix ./conda_mob_suite_env --file mob_suite_environment.yml Collecting package metadata (repodata.json): done Solving environment: done Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(698): An error occurred while installing package 'bioconda::mob_suite-3.0.3-pyhdfd78af_0'. Rolling back transaction: done

LinkError: post-link script failed for package bioconda::mob_suite-3.0.3-pyhdfd78af_0 location of failed script: /home/tools/conda_mob_suite_env/bin/.mob_suite-post-link.sh ==> script messages <==

==> script output <== stdout: stderr: Traceback (most recent call last): File "/home/tools/conda_mob_suite_env/bin/mob_init", line 7, in from mob_suite.mob_init import main File "/home/tools/conda_mob_suite_env/lib/python3.8/site-packages/mob_suite/mob_init.py", line 8, in from mob_suite.blast import BlastRunner File "/home/tools/conda_mob_suite_env/lib/python3.8/site-packages/mob_suite/blast/__init__.py", line 8, in import pandas as pd File "/home//.local/lib/python3.8/site-packages/pandas/__init__.py", line 22, in from pandas.compat.numpy import ( File "/home/.local/lib/python3.8/site-packages/pandas/compat/numpy/__init__.py", line 20, in raise ImportError( ImportError: this version of pandas is incompatible with numpy < 1.16.5 your numpy version is 1.16.4. Please upgrade numpy to >= 1.16.5 to use this pandas version return code: 1 ()
Anto007 commented 2 years ago

Btw, I'm using miniconda3 and conda 4.9.2

Anto007 commented 2 years ago

never mind I took the pip route for installing within a python 3.7 env

kbessonov1984 commented 2 years ago

Glad to hear it work the other way. It seems you had an old numpy library installed in the Conda environment that caused this pandas and numpy issue:

ImportError:this version of pandas is incompatible with numpy < 1.16.5 your numpy version is 1.16.4. Please upgrade numpy to >= 1.16.5 to use this pandas version

Will update Conda recipe to explicitly ask for numpy 1.16.5 and above