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Installation following README doesn't work

See original GitHub issue

Hopefully this will be fixed in #1871 As a reference I record the problem I am facing with. Currently I cannot install deepchem either by pip or by conda. The CI was broken where installation is by the scripts:

conda install -y -q scikit-learn=0.22
conda install -y -q -c deepchem -c rdkit -c conda-forge -c omnia deepchem=2.3.0

The error was that tensorflow is not installed. So did you remove the dependency from anaconda in 2.3.0?

By the way, I tried using pip but failed (#1842)

pip install scikit-learn==0.22 && \
conda install -y -c rdkit rdkit && \
pip install joblib pandas tensorflow pillow deepchem

but the output was

ImportError: cannot import name 'NewCheckpointReader' from 'tensorflow.python.pywrap_tensorflow_internal' (/miniconda/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py)

All these two ways were exactly the same as the document but nothing works. And a stable version is highly required including well defined dependencies. For example, scikit-learn should be <0.23 in deepchem 2.3.0 due to joblib (#1861)

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:5 (3 by maintainers)

github_iconTop GitHub Comments

1reaction
OXPHOScommented, Jul 9, 2020

Thank you. I reset my environment and started all over. Now everything worked.

BTW, one thing I am not sure whether it was important:

pip install tensorflow==1.14
conda install -c rdkit -c conda-forge rdkit deepchem==2.3.0

installed rdkit 20170901, in which I could not use rdkit.Chem.Draw(see the issue) So I unsintalled rdkit and did conda install -c conda-forge rdkit to get the 2020.03.4 version.

So far so good.

Maybe this would be useful to someone.

1reaction
nissy-devcommented, Jun 2, 2020

Sorry for your inconvinience 🙇‍♂️ Maybe you can install by using the following command. deepchem v2.3.0 requires tensorflow v1.

pip install scikit-learn==0.22 && \
conda install -y -c rdkit rdkit && \
pip install joblib pandas tensorflow==1.15 pillow deepchem
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