Connecting forever after installation

[quantaosun]

After installation, the system try to restart but then the status stays on connecting state.

[jaimergp]

Is this happening consistently in several notebooks or is it a one-off thing? In other words, can you reproduce this and in that case, can you share a notebook with the problem you are describing? Thanks!

[Owaiskhan9654]

It get hangs while Solving environment after creating Conda env. This issue is persistence. @jaimergp

[jaimergp]

Can you use mamba instead of conda in your command?

[Owaiskhan9654]

Also get this warning in Condacolab installation logs.

WARNING: You currently have a PYTHONPATH environment variable set. This may cause unexpected behavior when running the Python interpreter in Mambaforge. For best results, please verify that your PYTHONPATH only points to directories of packages that are compatible with the Python interpreter in Mambaforge: /usr/local

[quantaosun]

Hi all, Here is an example that I have always been able to repeat the error. https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb

Cheers

Owais Ahmad @.***> 于2023年6月19日周一 21:34写道：

Also get this warning in Condacolab installation logs.

WARNING: You currently have a PYTHONPATH environment variable set. This may cause unexpected behavior when running the Python interpreter in Mambaforge. For best results, please verify that your PYTHONPATH only points to directories of packages that are compatible with the Python interpreter in Mambaforge: /usr/local

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[jaimergp]

I would rewrite the install code as follows for better performance:

        !wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.0/vina_1.2.0_linux_x86_64 -O vina
        !chmod u+x vina

        !pip install condacolab
        import condacolab
        condacolab.install_mambaforge()  # includes mamba

And in a new cell:

        !mamba install -c conda-forge -c bioconda mgltools=1.5.7 biopython=1.78 \
        openbabel=3.1.0 plip=2.2.2 zlib=1.2.11 xlsxwriter=3.0.3
        !pip install py3Dmol==2.0.0.post2 pybel==0.15.5 rdkit-pypi==2022.3.5

Otherwise you don't allow time for the kernel to restart and things might break. So wait until the kernel has restarted and then do the mamba installs.

[jaimergp]

The problem with your notebook is that it silently ignores errors (and puts stdout in a log, so you don't see things as they happen). Your mamba code fails because colab runs now on Python 3.10 and those package versions are not available for this Python release:

The following packages are incompatible
├─ biopython 1.78**  is uninstallable because there are no viable options
│  ├─ biopython 1.78 would require
│  │  └─ python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported;
│  ├─ biopython 1.78 would require
│  │  └─ python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported;
│  ├─ biopython 1.78 would require
│  │  └─ python >=3.8,<3.9.0a0 , which conflicts with any installable versions previously reported;
│  └─ biopython 1.78 would require
│     └─ python >=3.9,<3.10.0a0 , which conflicts with any installable versions previously reported;
├─ openbabel 3.1.0**  is uninstallable because there are no viable options
│  ├─ openbabel 3.1.0 would require
│  │  └─ python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported;
│  ├─ openbabel 3.1.0 would require
│  │  └─ python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported;
│  └─ openbabel 3.1.0 would require
│     └─ python >=3.8,<3.9.0a0 , which conflicts with any installable versions previously reported;
└─ zlib 1.2.11**  is requested and can be installed.

[quantaosun]

I should have looked at the log. It helps a lot, thanks!

jaimergp @.***> 于2023年6月20日周二 17:17写道：

The problem with your notebook is that it silently ignores errors (and puts stdout in a log, so you don't see things as they happen). Your mamba code fails because colab runs now on Python 3.10 and those package versions are not available for this Python release:

The following packages are incompatible ├─ biopython 1.78 is uninstallable because there are no viable options │ ├─ biopython 1.78 would require │ │ └─ python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported; │ ├─ biopython 1.78 would require │ │ └─ python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported; │ ├─ biopython 1.78 would require │ │ └─ python >=3.8,<3.9.0a0 , which conflicts with any installable versions previously reported; │ └─ biopython 1.78 would require │ └─ python >=3.9,<3.10.0a0 , which conflicts with any installable versions previously reported; ├─ openbabel 3.1.0 is uninstallable because there are no viable options │ ├─ openbabel 3.1.0 would require │ │ └─ python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported; │ ├─ openbabel 3.1.0 would require │ │ └─ python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported; │ └─ openbabel 3.1.0 would require │ └─ python >=3.8,<3.9.0a0 , which conflicts with any installable versions previously reported; └─ zlib 1.2.11** is requested and can be installed.

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[nigh8w0lf]

In case anyone else has this issue, for me it was because of Installing directly from the git Main branch. When I installed the package instead from pypi there were no issues.