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.
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.