Your whonix setup could complain about nonfree packages, even if you have 
already uninstalled them: "Non-free packages with status other than installed" 
VRMS error message from whonixcheck script (Whonix-Check).

The only answer I've found about what to do in this situation is "sudo apt-get 
clean" - but it either didnt solve this issue at all, or solved it only 
partially (not completely!), and so I still was getting this issue even though 
I have removed this non-free package long time ago...

However, the following command has helped me to finally fix this problem:

sudo apt-get --purge remove <package_name>

For example:

sudo apt-get --purge remove libfaac0

(libfaac0 is the only non free package I have accidentally encountered during 
the recent days)

Hope that helps!

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