google-deepmind / google-deepmind/alphafold

Colab AlphaFold cannot install third-party software

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Description

Hi! I was trying to use the jupyter notebook on Colab and I could not pass the cell 1. It seems to get stuck on line 22. I stop the cell manually and here is the output:
```
Found existing installation: tensorflow 2.12.0
Uninstalling tensorflow-2.12.0:
Successfully uninstalled tensorflow-2.12.0
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
libdivsufsort3
Suggested packages:
hmmer-doc
The following NEW packages will be installed:
hmmer libdivsufsort3
0 upgraded, 2 newly installed, 0 to remove and 16 not upgraded.
Need to get 1,198 kB of archives.
After this operation, 7,621 kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libdivsufsort3 amd64 2.0.1-5 [42.8 kB]
Get:2 http://archive.ubuntu.com/ubuntu jammy/universe amd64 hmmer amd64 3.3.2+dfsg-1 [1,155 kB]
Fetched 1,198 kB in 0s (2,693 kB/s)
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 78, <> line 2.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (This frontend requires a controlling tty.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin:
Selecting previously unselected package libdivsufsort3:amd64.
(Reading database ... 120831 files and directories currently installed.)
Preparing to unpack .../libdivsufsort3_2.0.1-5_amd64.deb ...
Unpacking libdivsufsort3:amd64 (2.0.1-5) ...
Selecting previously unselected package hmmer.
Preparing to unpack .../hmmer_3.3.2+dfsg-1_amd64.deb ...
Unpacking hmmer (3.3.2+dfsg-1) ...
Setting up libdivsufsort3:amd64 (2.0.1-5) ...
Setting up hmmer (3.3.2+dfsg-1) ...
Processing triggers for man-db (2.10.2-1) ...
Processing triggers for libc-bin (2.35-0ubuntu3.1) ...
/sbin/ldconfig.real: /usr/local/lib/libtbb.so.12 is not a symbolic link

/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc.so.2 is not a symbolic link

/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc_proxy.so.2 is not a symbolic link

/sbin/ldconfig.real: /usr/local/lib/libtbbbind_2_5.so.3 is not a symbolic link

/sbin/ldconfig.real: /usr/local/lib/libtbbbind_2_0.so.3 is not a symbolic link

/sbin/ldconfig.real: /usr/local/lib/libtbbbind.so.3 is not a symbolic link

Collecting py3dmol
Downloading py3Dmol-2.0.3-py2.py3-none-any.whl (12 kB)
Installing collected packages: py3dmol
Successfully installed py3dmol-2.0.3
PREFIX=/opt/conda
Unpacking payload ...

Installing base environment...

Downloading and Extracting Packages

Downloading and Extracting Packages

Preparing transaction: done
Executing transaction: done
installation finished.
WARNING:
You currently have a PYTHONPATH environment variable set. This may cause
unexpected behavior when running the Python interpreter in Miniconda3.
For best results, please verify that your PYTHONPATH only points to
directories of packages that are compatible with the Python interpreter
in Miniconda3: /opt/conda
env: PATH=/opt/conda/bin:/opt/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-sdk/bin
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

environment location: /opt/conda

added / updated specs:
- conda==23.5.2

The following packages will be downloaded:

package | build
---------------------------|-----------------
certifi-2023.7.22 | py311h06a4308_0 154 KB
openssl-3.0.10 | h7f8727e_0 5.2 MB
------------------------------------------------------------
Total: 5.3 MB

The following packages will be UPDATED:

certifi 2023.5.7-py311h06a4308_0 --> 2023.7.22-py311h06a4308_0
openssl 3.0.9-h7f8727e_0 --> 3.0.10-h7f8727e_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: ...working... unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): ...working... failed

CondaError: KeyboardInterrupt
```

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