BioPerl uses many modules that you might not have installed. From BioPerl INSTALL file:
Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a few failed tests may not affect your usage of BioPerl
Most of the time you will not need these additional modules depending on what modules within BioPerl you are using. I'm sure that BioPerl has installed correctly on you system. I would work through http://www.bioperl.org/wiki/HOWTO:Beginners to learn BioPerl. If you get errors running these basic codes in the HOWTO, repost another question.
Good luck,
Paul