It's been awhile since I've recompiled, but my guess is that the error
make[1]: mex: Command not found
means that you need to edit the makefile (probably "Makefile.var") to tell it where the matlab "mex" command is.
For example, for my Makefile.var, I replaced the line
MEXBIN = mex
with the line
MEXBIN = /opt/matlab-14sp3/bin/mex
which is the location on my machine.
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