Can you please talk us through exactly how to reproduce the issue?
I have used u-u with a wide variety of other apt frontends in 16.04 without
seeing that problem yet.
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Touch seeded packages, which is subscribed to unattended-upgrades in
Unable to remove packages that become unused in conjunction with
updating by other software
Status in unattended-upgrades package in Ubuntu:
When using default settings for unattended-upgrades i.e.
U-U is unable to remove packages that become unused in conjunction with
updating by other software such as update-manager or apt full-upgrade. This is
because U-U compares the list of unneeded packages before and after it upgrades
packages to detect which packages are new unused ones.
DistroRelease: Ubuntu 16.04
Package: unattended-upgrades 0.90
ProcVersionSignature: Ubuntu 4.4.0-36.55-generic 4.4.16
Uname: Linux 4.4.0-36-generic i686
Date: Sat Sep 17 11:28:44 2016
InstallationDate: Installed on 2016-09-05 (11 days ago)
InstallationMedia: Mythbuntu 16.04.1 LTS "Xenial Xerus" - Release i386
UpgradeStatus: No upgrade log present (probably fresh install)
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