|  Obvious example is libnet, if you initialize the CPAN stuff, it installs
|  libnet.

  The CPAN stuff and pkgsrc are conflicting package managing systems.
If you use pkgsrc, don't use CPAN or vice versa.

|  What is the best practice, here ? Reinstall via pkgsrc, possibly
|  overwriting a newer version, breaking a dependance in CPAN ?

  Updating or creating a pkg would be the most useful step here
I guess :-)

	mjl