On one of my cpanel boxes, I kept getting Deprecated warnings from PHP stemming from PEAR Config.php, Register.php and HTTP_Upload.php. When I logged into the cpanel control panel, it shoed that PEAR was up-to-date.
A quick look at the server showed me I have two PEAR installs. One at /usr/local/lib/php and one /usr/lib/php.
The solution is easy:
/usr/local/bin/pear -V /usr/bin/pear -V /usr/local/bin/pear upgrade PEAR /usr/bin/pear upgrade PEAR