X.org should not be in dependencies for python3 (just like they are not required for python package) apt-get install python3 Reading Package Lists... Done Building Dependency Tree... Done The following extra packages will be installed: fontconfig libX11 libX11-locales libXScrnSaver libXau libXdmcp libXext libXft libXrender libtcl libtk libxcb python3-base python3-modules-tkinter The following NEW packages will be installed: fontconfig libX11 libX11-locales libXScrnSaver libXau libXdmcp libXext libXft libXrender libtcl libtk libxcb python3 python3-base python3-modules-tkinter 0 upgraded, 15 newly installed, 0 removed and 0 not upgraded. Need to get 0B/6709kB of archives. After unpacking 31.9MB of additional disk space will be used.
Видимо это из-за того, что python3-base тянет за собой python3-modules-tkinter. Наверняка это не обязательно.
На данный момент уже починено.