In the "go-pear" auto-installation script, which is an interactive program using console I/O, several attempts are made to turn off output buffering, but none of them succeeds. It does (in this order)

ob_implicit_flush(true);
ini_set('implicit_flush', true);

But the output STILL does not get flushed. Because it relies on this behaviour in order to work, I cannot proceed.

The script which produces this error is (at the time of writing) at

http://pear.php.net/go-pear 

There are some other bug reports which are similar but they all seem to be related to other SAPIs.

I configured PHP with 

./configure  --prefix=/home/mark/apache/php --with-apxs=/home/mark/apache/bin/apxs --enable-cli --with-zlib

To build the Apache and CLI SAPIs.