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I have two installations of owncloud running. One is version 6.something, installed from the ubuntu repository. The other is version 7.something, upgraded from the version 6 ubuntu repository originally installed.

I came to work this morning to find out both had been "removed from ubuntu due to security issues".

Why had the installations been removed?

Why was the version not checked before removing them?

What can I do to prevent owncloud or other packages being removed when I'm not watching?

How can I tell apt-get that I still want to keep php5, mysql et al so that apt-get autoremove won't make my servers completely useless?

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According to the Launchpad publishing history of Owncloud, it was removed from the repositories because of bug report #1384355 by request of its upstream authors because of a severe security vulnerability. Thereafter a version with backported fixes has been published for Trusty 12h ago, but not (yet) for Utopic for some reason.

I recommend that you download and install the packages for Trusty manually until the issue has been resolved. Consider filing a bug report, if the package doesn't reappear in the Utopic repositories soon.

You can try apt-mark manual PACKAGE... (see man page) to flag some of Owncloud's dependencies as manually installed to remove them from the set of packages that apt-get autoremove would remove.

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