You have two versions of pear installed. The one you run, and the one you upgrade.
which pear
will return a different path than pear list-files pear|grep script
; that's your problem.
Either run the installed one (from list-files), or set the paths so that the which pear
-version gets updated (pear config-show
and pear config-set
).
See Can't install PHPUnit via PEAR, requires PEAR Installer >= 1.9.2, can't upgrade PEAR from 1.9.0 for more info.