this is what I did to get it to compile, had some errors with Jack at first, I might have compiled actually with portaudio on the most freshest install.
sudo apt-get build-dep puredata ./autogen.sh ./configure --disable-portaudio --enable-jack sudo make install
Done some recording with my desktop server. The soundcard in it is an Creative Audigy2 Platinum. The audio does not glitch with pd but the soundcard has a bad capacitor or something in it. I can touch the pins of a few different caps around C100 on the board and the background IR Radiation sounding like sizzling sound stops. Have soldering iron now so am searching for parts to replace. At aNy rate here is a recording with the fresh pd. thanks! and Enjoy https://archive.org/details/centaur-sh-mandelbox