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"InvalidVersionSpec" error - installation fails

See original GitHub issue

📚 Installation

Environment

OS: Ubuntu 18.04.4 LTS
Package manager (PyPI or Conda): Conda
Python version: 3.7.6
DeepChem version: 2.5.0
TensorFlow version: 2.3.0
PyTorch version (optional):
CUDA/cuDNN version (optional):
Any other relevant information: I would like to install from source with conda. I followed the instructions given here - with GPU.

Checklist

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

Additional context

The error I am getting is InvalidVersionSpec: Invalid version '5.4.104+': empty version component, when executing the command source scripts/install_deepchem_conda.sh 3.7 gpu. The log is given below:

Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.5
  latest version: 4.10.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /opt/conda/envs/deepchem

  added / updated specs:
    - python=3.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            1_gnu          22 KB  conda-forge
    ca-certificates-2020.12.5  |       ha878542_0         137 KB  conda-forge
    certifi-2020.12.5          |   py37h89c1867_1         143 KB  conda-forge
    ld_impl_linux-64-2.35.1    |       hea4e1c9_2         618 KB  conda-forge
    libffi-3.3                 |       h58526e2_2          51 KB  conda-forge
    libgcc-ng-9.3.0            |      h2828fa1_19         7.8 MB  conda-forge
    libgomp-9.3.0              |      h2828fa1_19         376 KB  conda-forge
    libstdcxx-ng-9.3.0         |      h6de172a_19         4.0 MB  conda-forge
    ncurses-6.2                |       h58526e2_4         985 KB  conda-forge
    openssl-1.1.1k             |       h7f98852_0         2.1 MB  conda-forge
    pip-21.0.1                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
    python-3.7.10              |hffdb5ce_100_cpython        57.3 MB  conda-forge
    python_abi-3.7             |          1_cp37m           4 KB  conda-forge
    readline-8.0               |       he28a2e2_2         281 KB  conda-forge
    setuptools-49.6.0          |   py37h89c1867_3         947 KB  conda-forge
    sqlite-3.35.4              |       h74cdb3f_0         1.4 MB  conda-forge
    tk-8.6.10                  |       h21135ba_1         3.2 MB  conda-forge
    wheel-0.36.2               |     pyhd3deb0d_0          31 KB  conda-forge
    xz-5.2.5                   |       h516909a_1         343 KB  conda-forge
    zlib-1.2.11                |    h516909a_1010         106 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        81.0 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_19
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_19
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_19
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  openssl            conda-forge/linux-64::openssl-1.1.1k-h7f98852_0
  pip                conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.7.10-hffdb5ce_100_cpython
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3
  sqlite             conda-forge/linux-64::sqlite-3.35.4-h74cdb3f_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010



Downloading and Extracting Packages
python-3.7.10        | 57.3 MB   | ############################################################################################################# | 100% 
zlib-1.2.11          | 106 KB    | ############################################################################################################# | 100% 
libgcc-ng-9.3.0      | 7.8 MB    | ############################################################################################################# | 100% 
libgomp-9.3.0        | 376 KB    | ############################################################################################################# | 100% 
ld_impl_linux-64-2.3 | 618 KB    | ############################################################################################################# | 100% 
certifi-2020.12.5    | 143 KB    | ############################################################################################################# | 100% 
openssl-1.1.1k       | 2.1 MB    | ############################################################################################################# | 100% 
wheel-0.36.2         | 31 KB     | ############################################################################################################# | 100% 
_libgcc_mutex-0.1    | 3 KB      | ############################################################################################################# | 100% 
ca-certificates-2020 | 137 KB    | ############################################################################################################# | 100% 
libffi-3.3           | 51 KB     | ############################################################################################################# | 100% 
python_abi-3.7       | 4 KB      | ############################################################################################################# | 100% 
sqlite-3.35.4        | 1.4 MB    | ############################################################################################################# | 100% 
_openmp_mutex-4.5    | 22 KB     | ############################################################################################################# | 100% 
ncurses-6.2          | 985 KB    | ############################################################################################################# | 100% 
readline-8.0         | 281 KB    | ############################################################################################################# | 100% 
libstdcxx-ng-9.3.0   | 4.0 MB    | ############################################################################################################# | 100% 
setuptools-49.6.0    | 947 KB    | ############################################################################################################# | 100% 
tk-8.6.10            | 3.2 MB    | ############################################################################################################# | 100% 
pip-21.0.1           | 1.1 MB    | ############################################################################################################# | 100% 
xz-5.2.5             | 343 KB    | ############################################################################################################# | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate deepchem
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - conda-merge


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-4.10.0               |   py37h89c1867_1         3.1 MB  conda-forge
    conda-merge-0.1.5          |             py_0           8 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.1 MB

The following NEW packages will be INSTALLED:

  conda-merge        conda-forge/noarch::conda-merge-0.1.5-py_0

The following packages will be UPDATED:

  ca-certificates                      2020.6.20-hecda079_0 --> 2020.12.5-ha878542_0
  certifi                          2020.6.20-py37hc8dfbb8_0 --> 2020.12.5-py37h89c1867_1
  conda                                4.8.5-py37hc8dfbb8_1 --> 4.10.0-py37h89c1867_1



Downloading and Extracting Packages
conda-4.10.0         | 3.1 MB    | ############################################################################################################# | 100% 
conda-merge-0.1.5    | 8 KB      | ############################################################################################################# | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing DeepChem in the GPU environment
Collecting package metadata (repodata.json): failed

InvalidVersionSpec: Invalid version '5.4.104+': empty version component

Issue Analytics

State:
Created 2 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

ashok-arjuncommented, May 16, 2021

Update:

This error was solved when I installed deepchem inside the base conda environment. I’m not sure why, but it solved the problem.

0reactions

ashok-arjuncommented, May 13, 2021

Output suggests that you run conda update -n base conda to update conda. Can you try that @ashok-arjun and run it again to see if updating fixes the issue? If not, I can try to investigate

Thanks. I tried updating conda, but it still gave the same error.

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