You should query for the updates some minutes after the session is
started and after the org.freedesktop.PackageKit.UpdatesChanged()
signal has been emitted. There is no need anymore to query for updates
after each completed transaction. The signal gets emitted by
packagekit/aptdaemon after each transaction which would change the
number of available updates.

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https://bugs.launchpad.net/bugs/903756

Title:
  Use PackageKit interface to aptdaemon

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