Public bug reported:

It seems that if synaptic is installing automatic updates / security
updates in the background and you ask ubuntu (through X) to turn off the
computer your package system can get corrupted.

My suggestion is that when selecting logout/shutdown/hibernate etc. a
message should appear showing something like:

Your system is being updated

[************                         ] "Progress bar"

You will be logged out / The sytem will shutdown/hibernate etc. when it
is finished installing...

If you wish to override, press "button"

** Affects: synaptic (Ubuntu)
     Importance: Undecided
         Status: New

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Prevent shutdown/logout when package manager / update manager is working
https://bugs.launchpad.net/bugs/197255
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