https://launchpad.net/ubuntu/karmic/i386/autoconf

This page says:

"This version of autoconf is not compatible with scripts meant for
 Autoconf 2.13 or earlier. If you need support for such scripts,
 you must also install the autoconf2.13 package."

If you choose install autoconf2.13 package in addition to the 2.64, then
the default autoconf executable(s) are changed to the 2.13 versions. The
newest autoconf2.64 becomes a secondary, and accessible as
'autoconf2.64'. When you uninstall 2.13, then the 2.64 is put back as
the primary again.

So perhaps autoconf2.13 can be added as a php5 build - time dependency.
Needs testing.

-- 
karmic: Compiling php fails with autoconf 2.64
https://bugs.launchpad.net/bugs/411890
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