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Under my Debian Jessie system, when I run aptitude I can see a lot of libraries not manually installed but without the automatic flag. So if I remove the main packages the dependent packages will stay.

aptitude screenshot

My question is the following: why theses not manually installed packages are not marked with the automatic flag?

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I have had the same problem for years, for fresh installs, a lot of libraries are not set to auto although I see no reason for them not to. I have been setting auto on all libraries manually, but once or twice I ran into problems because something important was uninstalled thereafter (once it was a pam module I think :( ).

So I'm not sure if it is a good idea to mark every library as auto by hand. If you do, I recommend the following procedure:

  1. make a complete backup of your system (always a good idea!).
  2. save a list of installed packages (for example dpkg -l > installed_packages.txt).
  3. mark all libraries as auto where you think it's not a problem (risky!) and let aptitude uninstall some of them.
  4. reboot and see if everything works as expected.
  5. if not, reinstall all packages that were uninstalled and figure out which were really important.
  6. If system is unbootable, use the backup.

That being said, I have been doing this for a long time and did not run into many problems. I wish there was an official Debian guide / answer why this is so in the first place, but I have not been able to find one. If anyone has a pointer to something that helps solving this problem / give a better answer I were really grateful myself!

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I'm guessing it's the same for Debian, but on Ubuntu, at least, the packages that are installed by default (when Debian/Ubuntu was first installed) don't have the automatically-installed mark. The libraries you're looking at were likely installed at the time of the Debian installation.

  • Looking at the packages listed, that seems unlikely. – Faheem Mitha Feb 1 '15 at 17:43

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