This documentation is not using the current rendering mechanism and is probably outdated. The extension maintainer should switch to the new system. Details on how to use the rendering mechanism can be found here.
A list of all changes can be found on GitHub https://github.com/derhansen/sf_yubikey/commits/master
Since version 1.0.0, YubiKey OTP validation is only handled through the bundled class YubikeyAuth. The usage of PEAR classes has been removed.