For the Synaptic message complaining about
/var/cache/apt/archives/partial, setting the owner of that directory to
_apt seems to avoid it, based on my tests in a VirtualBox VM of Wily
upgraded to Xenial.

I haven't (yet) encountered an error complaining about
/root/.synaptic/[…]. It seems really bizarre that it would insist on
some system user being able to access something in root's home
directory.

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https://bugs.launchpad.net/bugs/1522675

Title:
  /root/.synaptic/ not created

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