If you wish to install Pear for cPanel PHP (native PHP version) for some user, then you can use the standard way provided by WHM/cPanel, but if the alt-PHP (PHP Selector) is used, then you (as root or as an user) need to install necessary Pear modules by using pear for current user php like this:
# /opt/alt/phpXX/usr/bin/pear install moduleName
where XX is PHP version (for example 71 for PHP 7.1).
In this case include_path will contain the value "/opt/alt/php71/usr/share/pear"
Alternatively, you can set it manually in /opt/alt/php71/etc/php.ini directly (PHP 7.1 as an example):
include_path = ".:/usr/share/pear:/opt/alt/php71/usr/share/php:/opt/alt/php71/usr/share/pear"