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I want to upgrade from Ubuntu 16.04.5 LTS to 18.04, so ran sudo do-release-upgrade.
After downloading and extracting bionic.tar.gz I get:

Can not upgrade 



Your python3 install is corrupted. Please fix the '/usr/bin/python3' 

symlink.

I saw How to fix "python installation is corrupted"? and so I did sudo ln -sf /usr/bin/python3.6 /usr/bin/python3 thinking that it would be a similar problem. But that didn't work (still same error message).

I have a few python versions:

ls /usr/lib | grep python

python2.7

python3

python3.5

python3.6



update-alternatives --display python3

python3 - auto mode

  link best version is /usr/bin/python3.6

  link currently points to /usr/bin/python3.6

  link python3 is /usr/bin/python3

/usr/bin/python3.5 - priority 1

/usr/bin/python3.6 - priority 2

How do I fix python3?

You need to use the default Python 3 version for 16.04. That's 3.5, not 3.6. So run:

sudo ln -sf /usr/bin/python3.5 /usr/bin/python3

If that doesn't work, try reinstalling the python3 package.

sudo apt-get install --reinstall python3

By the way, update-alternatives --display python3 should give you update-alternatives: error: no alternatives for python3. Different versions of Python are not alternatives in Ubuntu.

I just ran into this problem on Pop!_OS 18.04, trying to upgrade to 18.10, and it turns out that the problem lay in the symlink for /usr/bin/python and not for /usr/bin/python3. I had had /usr/bin/python3.6 configured as an alternative for python (not python3), and when I changed this, then I could run do-release-upgrade as expected.

I wish the error message pointed to python and not python3.

Before, with the problem:

$ update-alternatives --display python

python - manual mode

  link best version is /usr/bin/python3.6

  link currently points to /usr/bin/python2.7

  link python is /usr/bin/python

/usr/bin/python2.7 - priority 1

/usr/bin/python3.6 - priority 2 

I fixed it this way:

$ sudo update-alternatives --remove-all python

$ sudo ln -sf /usr/bin/python2.7 /usr/bin/python

Basically the solution to this problem consists of making /usr/bin/python point to the right version of Python your Ubuntu release expects (for instance, in 16.04 was Python2.7 and in 18.04 was Python3.6).

If you have several versions of Python installed in your system, you might be using update-alternatives to manage them. It doesn't matter much your default alternative for Python is the right version your system expects (3.6 in Ubuntu 18.04), it won't work.

The reason why this doesn't work is that, when using update-alternatives, /usr/bin/python3 points to /etc/alternatives/python3, and it seems that's not exactly the same as making /usr/bin/python3 point to /usr/bin/python3.6.

That's why the solution to this problem often consists of stop managing your Python3 versions with update-alternatives and make /usr/bin/python3 point to the right version of Python3 your system expects.