Easiest way to fix that is to copy these files to the directory you're compiling in:
cp /usr/share/libtool/config.guess .
cp /usr/share/libtool/config.sub .
cp /usr/share/libtool/ltmain.sh .
cp /usr/share/automake-1.6/install-sh .
cp /usr/share/automake-1.6/missing .
cp /usr/share/automake-1.6/mkinstalldirs .
Note, you don't have to copy all of them. If you don't already have a file with the same name in the source directory, then you can skip that one. These are more up to date files than the ones the source comes with, and they should work to compile the source.
Just so you know, the config.guess and config.sub files are the ones that you definitely need - they'll be able to guess the host type correctly.