question-mark
Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

DeepChem COLAB installation fails

See original GitHub issue

📚 Installation

Environment

  • OS: Ubuntu 18.04.5 LTS
  • Package manager (PyPI or Conda): Conda
  • Python version: 3.7
  • DeepChem version: As defined in https://raw.githubusercontent.com/deepchem/deepchem/master/scripts/colab_install.py
  • TensorFlow version: NA
  • PyTorch version (optional):
  • CUDA/cuDNN version (optional):
  • Any other relevant information: Google COLAB

Checklist

  • [ x ] I followed the installation guide.
  • [ x ] I used Google Colab.
  • [ ] I do have multiple CUDA versions on my machine.

Additional context

Ran the following tutorial in COLAB https://github.com/deepchem/deepchem/blob/master/examples/tutorials/06_Introduction_to_Graph_Convolutions.ipynb

!curl -Lo conda_installer.py https://raw.githubusercontent.com/deepchem/deepchem/master/scripts/colab_install.py
import conda_installer
conda_installer.install()
!/root/miniconda/bin/conda info -e

It gave me the following error. A few weeks ago, the code worked fine.

% Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  3501  100  3501    0     0  43762      0 --:--:-- --:--:-- --:--:-- 43762
python version: 3.7.11
remove current miniconda
fetching installer from https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
done
installing miniconda to /root/miniconda
done
installing rdkit, openmm, pdbfixer
added conda-forge to channels
added omnia to channels
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
<ipython-input-5-0b37ae099887> in <module>()
      2 get_ipython().system('curl -Lo conda_installer.py https://raw.githubusercontent.com/deepchem/deepchem/master/scripts/colab_install.py')
      3 import conda_installer
----> 4 conda_installer.install()
      5 get_ipython().system('/root/miniconda/bin/conda info -e')

1 frames
/content/conda_installer.py in install(chunk_size, file_name, url_base, conda_path, add_python_path, additional_channels, additional_packages)
    121       "--yes",
    122       "python=={}".format(python_version),
--> 123       *packages,
    124   ])
    125   logger.info("done")

/usr/lib/python3.7/subprocess.py in check_call(*popenargs, **kwargs)
    361         if cmd is None:
    362             cmd = popenargs[0]
--> 363         raise CalledProcessError(retcode, cmd)
    364     return 0
    365 

CalledProcessError: Command '['/root/miniconda/bin/conda', 'install', '--yes', 'python==3.7.11', 'rdkit=2020.09.02', 'pdbfixer', 'openmm']' returned non-zero exit status 1.

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:7 (2 by maintainers)

github_iconTop GitHub Comments

3reactions
ph-mehdicommented, Aug 1, 2021

Try this:

! pip install rdkit-pypi

1reaction
ravichascommented, Jul 22, 2021

@VIGNESHinZONE Thank you for sharing the notebook

Read more comments on GitHub >

github_iconTop Results From Across the Web

Error running colab tutorial notebook(s) · Issue #2727 - GitHub
Steps to reproduce the behavior: Run first cell in notebook ... CalledProcessError: Command '['/root/miniconda/bin/conda', 'install', '--yes', ' ...
Read more >
Getting DeepChem running in Colab - Community
I've recently started hacking with DeepChem in Colab. ... I hope to be use Colab notebook as I often have problem installing Deepchem...
Read more >
deepchem/Lobby - Gitter
I tried to install using conda install -c deepchem=2.1.0 python = 3.7 ( I also used python ... For everyone with installation problems,...
Read more >
Installation — deepchem 2.6.2.dev documentation
Install deepchem via pip or conda by simply running, ... The fastest way to get up and running with DeepChem is to run...
Read more >
Tutorial Part 18: Using Reinforcement Learning to Play Pong
Setup. To run DeepChem within Colab, you'll need to run the following cell of ... To install gym you should also use pip...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found