After a bit more research I found out that the following commit [1] is causing the automake build failure:
commit 496c888ebdddbc29ec042ff5e3137cfd0df80281 Author: Miller Puckette msp@ucsd.edu Date: Tue Jun 18 19:06:29 2013 -0700
Portaudio tp 2013/06/19 snapshot
if I do:
$ git pull origin master $ git revert 496c888 $ ./autogen.sh $ ./configure $ make
pd builds fine...
[1] http://sourceforge.net/p/pure-data/pure-data/ci/496c888ebdddbc29ec042ff5e313...
cheers, y