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I'm running a Debian web server. Though the packages are up-to-date, current vulnerability detection software (for instance Nessus) found several potential security risks that exist in the software provided by these packages -- my greatest concerns being Apache and PHP.

I'm planning to work around this by compiling them myself from source, but I'm not really sure about the steps I should take first. Should I uninstall Apache/PHP packages before installing from source? What about their dependencies?

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The very first thing to do is to check the changelogs for the packages to be certain that they haven't been patched for the vunerabilit(y/ies) already; several vendors backport security patches to older versions.

Once you've done that, you should uninstall the system packages so that there is less confusion as to which version is being run. Unfortunately you will usually have to deal with the packages that depend on them yourself, building from source as required.

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