Set proxies in Gnome "Network Proxy Setting", or in /etc/bash.bashrc, or /etc/wget.rc won't apply to Update Manager.
You had to put a line like this in /etc/apt/apt.conf
Acquire::http::Proxy "http://proxy.mydomain.com:8080"
In "Breezy Badger" you must edit apt.conf as follows:
Acquire
{
http::proxy "http://proxy.mydomain.com:8080"
}
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