apt.conf "Acquire::http:Proxy "proxyserver:port" seems not to be used (Ubuntu 13.04 under Virtual Box on Win7)

Based on my past experience, overall Ubuntu (GNOME) doesn't work very well with PAC (Automatic Config). Pac (Proxy Auto-config) is basically JavaScript logic to determine the closest or most appropriate proxy for you, I strongly recommend using the proxy servers directly (in your case Network - Network Proxy).

A few things to check

Check your /etc/apt/apt.conf

Network -Network Proxy GUI will update /etc/apt/apt.conf and set the proxy info there.

Find out the proxy server info from pac

You can find the details by reading the proxy.pac file anyway.

So the /etc/apt/apt.conf should look like below (suppose the proxy server is => proxy.company.com port 80), do NOT use pac URL.

Acquire::http::proxy "http://proxy.company.com:80/";
Acquire::https::proxy "https://proxy.company.com:80/";
Acquire::ftp::proxy "ftp://proxy.company.com:80/";

NOTE: If no proxy is specified in the apt config files, apt-get will fall back to http_proxy environment variable.

From apt.conf man page, respond to the comment from @Braiam

   http
       HTTP URIs; http::Proxy is the default http proxy to use. It is in
       the standard form of http://[[user][:pass]@]host[:port]/. Per host
       proxies can also be specified by using the form http::Proxy::<host>
       with the special keyword DIRECT meaning to use no proxies. If no
       one of the above settings is specified, http_proxy environment
       variable will be used.

Check proxy environment variables

You can check proxy settings by running the following in terminal

echo $http_proxy
echo $https_proxy
echo $ftp_proxy

If you set env variables correctly, you should be should be able to update in CLI.

Prefer IPv4

I noticed apt-get was trying to connect to the update servers using their ipv6 address. This could cause problems (sometimes the IPV6 addresses expire or change).

You can edit /etc/gai.conf and add precedence ::ffff:0:0/96 100 to prefer ipv4 over ipv6.

More details

• https://unix.stackexchange.com/a/13263/30622
• https://serverfault.com/a/177649/145918

I believe I have had this very problem and the answer is simple. The syntax is critical. It must look like this:

Acquire::http::Proxy "http://x.y.z.251:9090";

(There is an extra ":" and a terminating ";")