Some systems like Debian have some strong conventions for how the integrate Perl into the larger operating system. Setting up and getting CPAN working smoothly on those systems is non-trivial.
Quite the contrary. The cpan shell works out-of-the-box on Debian systems, and doesn't conflict with the package manager at all.
And not only does Debian come with lots of perl modules as .deb packages, it also allows fairly easy generation of .deb packages from CPAN and custom perl modules via dh-make-perl or cpan2dist (distributed with CPANPLUS and thus with newer perl version in core).
And there's nothing easier in Debian than installing a .deb module (especially if you set up a mirror on your own and put them up there).
So if you want to solve the deployment problem on Debian based Linux distributions, you can get a clean solution pretty fast.
(I guess the same holds true for many other distributions, but I just talk about Debian because I'm familiar with it).
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