Following exactly the step-by-step instructions in these forums for converting to CustomBuiild 2 I ran into these errors, which stopped as shown.
Failed loading /usr/local/lib/ioncube_loader_lin_5.3.so: /usr/local/lib/ioncube_loader_lin_5.3.so: undefined symbol: php_body_write Zend Guard Loader requires Zend Engine API version 220090626. The Zend Engine API version 220100525 which is installed, is newer. Contact Zend Technologies at http://www.zend.com/ for a later version of Zend Guard Loader. Fatal error: Directive 'allow_call_time_pass_reference' is no longer available in PHP in Unknown on line 0 make: *** [install-pear-installer] Error 1 make: *** [install-pear] Error 2