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Can I uninstall package if it was installed not via the standard configure/make installation procedure:
$ sudo make install
but via running setup script in src directory?
$ sudo python setup.py install
Simple answer, no. You'll need to delete the files and folders created by the compilation process. There is a way of doing what you want but it involves installing the package checkinstall and then using it after the compilation phase.
I use checkinstall when I compile my own software from source. It makes things much easier if I want to remove the program at some point. I just treat it as a package and get rid of it via the "sudo aptitude remove <name of program>" command. I am prompted to supply a package name by checkinstall during the installation process. It works a treat.