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This is expected, as Python 2 is EOL, and so a number of libraries have taken it upon themselves to warn their users about that.
In this case it's setuptools. But you can run into the same thing with others.
When I did on my different system, I didn't received this ?
it could be that a version of certain dependencies which start printing these warnings hasn't been installed on the system on which you did not see the error.
In any case: ROS Noetic will no longer support/require Python 2 -- it'll exclusively depend on Python 3.
You will not see those warnings any more then.
Edit: alternatively, you could try installing python3-rosdep (which will require python3-catkin-pkg, python3-rosdep-modules and python3-rospkg). This is the Python3-version of rosdep. However, it may be a bit involved to get that installed on systems with ROS Kinetic already installed.
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