Having had some problems with audio drop outs in Ubuntu, I am now giving Sabayon 14.01 a try. I'm trying to compile Pd, ./autogen.sh seemed to work fine, but when I type ./configure --enable-jack things go wrong. At the end of configure I get these messages:
./configure: line 15417: syntax error near unexpected token `JACK,'
./configure: line 15417: `    PKG_CHECK_MODULES(JACK, jack, have_jack=yes, have_jack=no)'
configure: error: ./configure failed for portaudio

I checked line 15417 in configure, but doesn't make any sense to me, unfortunately..

plus some other stuff that don't seem write (out of intuition, not knowledge or experience) for example:
checking machine/soundcard.h usability... no
checking machine/soundcard.h presence... no
checking for machine/soundcard.h... no
checking for _oss_ioctl in -lossaudio... no

I also got lots of warnings when I typed make, like:
msgfmt --check --tcl --locale=af -d . af.po
af.po:6: warning: header field 'Language' missing in header

Don't know if this helps, the messages from configure are quite a lot, I could post them if it's more helpful. I have Jack1 installed (there might be some issues there with memory allocation, but that should go to Jack's list, don't know if this influences Pd's compilation) and ALSA.
I've been posting a lot on this Linux and Pd issue of mine lately, but I do wanna give this combination a try...sorry if I irritate anyone..