Thanks for your bugreport.
update-manager should honor apt.conf. Could you please check if it was
just some bits that got downloaded without the proxy or if it was all
packages. The logs in /var/log/dist-upgrade/ and the apt-cacher logs
should help diagnoising this.
** Changed in: update-manager (Ubuntu)
Status: New => Incomplete
** Changed in: update-manager (Ubuntu)
Assignee: (unassigned) => Michael Vogt (mvo)
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update-manager doesn't honor apt.conf Proxy setting
https://bugs.launchpad.net/bugs/361554
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