libtool: Version mismatch error.

If you port and compile across Fedora and Ubuntu Gnu/Linux distros, you might find this bug between recent Ubuntu 16X and Fedora 20X versions of autotools.

libtool: Version mismatch error.  This is libtool 2.4.6 Debian-2.4.6-0.1, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6 Debian-2.4.6-0.1

I compiled on Ubuntu, then make maintainer-clean, then copied file folder over to a Fedora machine. Then any variation of 

rm aclocal.m4

autoreconf -fvi

aclocal --force --install

autoconf --force

libtoolize --force --copy

rm libtool 

rm autom4te.cache/*

does not clear out some of the cruft of the Ubuntu build environment. I tried many versions and stripped files out, but it still reinstalls the improper libtool in the source directory.

The only fix I could make work was to remove the libtool file after reconfiguration and then install the /usr/local/bin/libtool of that machine directly into build directory. Then libtool would work normally.

The cause could be any number of causes including timestamp differences on many machines ( some are on differing NTP servers), autotools mismatch, and probably make maintainer-clean doesn't remove enough cached files.