(Note: I'm running Ubuntu 9.10 on i386.)
I've installed a great many modules from CPAN using sudo cpan. I've installed a great many .deb packages using appropriate methods, some of which seem to contain Perl modules, too. I've also run into a spot of trouble (although I can't swear cpan has a thing to do with it) with conflicts between modules installed from these different sources. (Synaptic itself seems to rely on XML::SAX, for example.)
Various forum posts of dubious reliability and a buddy of mine suggest I never install any modules with cpan unless there is no alternative; rather, prefer to install only using Synaptic, apt-get, and friends.
What say the Monks?
Update: Great comments, thank you. I will leave the system perl and its libraries alone; if I install an application that requires modules, I'll let Synaptic take care of the dependencies. I'll compile a distinct development perl somewhere else and use cpan to install whatever I like there. I'll use the opportunity to consider different compilation flags, too.
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