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I am using Ruby for sysadmin ops but I was wondering what is the difference between

Fedora Ruby Package like : rubygem-thor-0.19.1-2.fc23.noarch

Ruby Gems like : thor (0.19.1) >> using gem list --local

and How to use the package and when?

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The ruby package is the "original" package created by any developer. The "rubygem" package is the one packaged and provided by fedora.

You should use the packages provided by fedora.... unless you need a version which isn't available for your needs, or when the package isn't available. The technical details of this can be found on packaging ruby.

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