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The cause of your problems probably pointed to in /opt/SageMath/logs/pkgs/python3-3.7.3.p1.log. It may or may not be related to the presence/absence of system packages ; however, Sage will (should) install a "local" version of missing system packages if necessary.

BTW, you may obtain better answer to questions about sage installation and possible bugs by posting your question to sage-support.