FYI, when I install a new version of the autotools, I do something like

# PATH=/new/path/bin:$PATH
# cd m4; ./configure --prefix=/new/path; make; make install
# cd ../autoconf; ./configure --prefix=/new/path; make; make install
# cd ../automake; ./configure --prefix=/new/path; make; make install
# cd ../libtool; ./configure --prefix=/new/path $OSXOPTS; make; make install

The proper versions of everything are found because they are first in PATH.

The OSXOPTS for libtool is needed because Apple ships another program named libtool. GNU libtool is renamed to glibtool (IIRC). There are a couple ways of effecting this. IIRC, I use a setting that prefixes the program with a g (something like --program-prefix=g).

Later,
Daniel

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