Mmm, you have to trust the Repo's your using .. certainly in the past some repos have been compromised and viruses have indeed made their way to user's PCs, but I think they try quite hard to keep them secure.
Just be a little bit careful if you download stuff from third party repos... doesn't matter what the application is, the installer runs as root, so if there is something nasty in the package, there's no real protection ...
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