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I believe both Pacman and Yaourt run a check over downloaded packages. Pacman outputs this as 'Checking package integrity' - whether or not that's the check I can't say for sure, but it seems likely.
Since Yaourt just acts as a frontend for Pacman on normal package ops, it doesn't actually do any checking itself unless you're pulling in a PKGBUILD from the AUR - then it'll check, provided the md5sum or similar are provided within the PKGBUILD.
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pacman, yaourt, md5
