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Error in installing mob_suite-3.0.0 (either by conda or pip3) - pandas EmptyDataError issue #63
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Dear Koji Yahara, Conda install error MOB-Suite v3.0.0Issue: Upon conda install the following import statement fails
Reason:
Meanwhile will update conda package explicitly restricting higher pandas versions and subsequently update code in Pip installation error MOB-Suite v3.0.0I got the same pandas related error via pip install and the remediation is again
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Thank you very much! Another environment caused the "Found conflicts!" error Thank you very much again. |
In a couple of days a new |
Thank you very much. I'm looking forward to the release of version 3.0.1. In a computing cluster system, in order to "have a separate conda environment for each tool", Many thanks again. |
Hello, yesterday a new mob_suite conda recipe was released fixing the With respect to separate environments I meant that it is better to have separate environment for each tool like The release of version |
Will mob_suite ever support |
@tseemann starting version 3.0.1 pandas version 1.1 and above is compatible as we moved |
Hi, I installed the software using pip but it gave me the EmptyDataError when running the program. Pandas version was 2.1.0. any solution? |
Yes, we do not support pandas 2.0 and above. Downgrade to version 1.5.3 inclusive or lower and all issues should disappear. This pandas version range is also in conda recipe. To support pandas 3.0 (that would be released soon), 2.0 and 1.0 we would require serious code overhaul as pandas library changes quite a lot between releases. |
Dear developers,
Thank you for developing mob-suite and making it pubic.
I'm eager to utilize it.
However, I'm facing the following errors in in installing
mob_suite-3.0.0 (either by conda or pip3).
Could you give me an advise how to fix it?
Thank you very much in advance.
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Error by conda
resulting in "ImportError: cannot import name 'EmptyDataError' from 'pandas.io.common'
although manual execution of "from pandas.io.common import EmptyDataError"
in the python 3 console doesn't cause any error.
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$ which conda
~/miniconda3/bin/conda
$ python --version
Python 3.7.3
$ conda create -c bioconda -n mob_suite mob_suite
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(700): An error occurred while installing package 'bioconda::mob_suite-3.0.0-py_1'.
Rolling back transaction: done
#######################################################################
Error by pip
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$ which pip
~/miniconda3/bin/pip
$ pip install --user mob_suite
ERROR: Command "/home/k-yahara/miniconda3/bin/python /home/k-yahara/miniconda3/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmp5gks5ebc" failed with error code 1 in /tmp/pip-install-1px41fwf/pyqt5
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Koji Yahara
Group Leader
Antimicrobial Resistance Research Center
National Institute of Infectious Diseases
Aoba-cho 4-2-1, Higashimurayama-shi, Tokyo
189-0002 Japan
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