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I used to update my packages via Apper but as it, unlike the Software Center, doesn't show popups when new updates are available I'd like to use the Software Center for updating.
And now I'm wondering if there's any substantial difference between using either of those for package-updates - especially from a security standpoint.

I already checked that both use the same repositories from the sources.list file but are there maybe other differences worth a note? Does either of them maybe have (or lack) some features that integrate with other software such as rkhunter or that verify packages or that write logs or anything of that sort?

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The vast majority of package management tools in Debian, including Apper and Software Center, end up using apt-provided implementations of the actual package management operations themselves, so anything which integrates with apt (such as rkhunter) will integrate with Apper and Software Center and other such tools.

In a little more detail, both Apper and Software Center rely on PackageKit to obtain information about packages and perform package installation, removal etc.; on Debian, PackageKit uses the apt libraries.

(When I say “vast majority” above, I’m being pedantic — the exceptions are tools such as rpm, which are available in Debian, but which you can’t use to manage the packages in a Debian system. In practice, you can consider that all package management tools in Debian do the right thing.)

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