This is possibly a duplicate post...

My build issue on Mac OS X on the autoconf step turned out to be two versions 
of autoconf on my system. Most of the build tools in /usr/local/bin were just 
links to tools in a "Cellar", but autoconf and a couple of others were not. My 
NuPIC build was successful after I linked to autoconf 2.69:

ln -s ../Cellar/autoconf/2.69/bin/autoconf ./autoconf

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