If you are receiving the following error when compiling mono 4.x “Version mismatch error. This is libtool 2.4.6, but the definition of this LT_INIT comes from libtool 2.4.2.”, then the aclocal.m4 file needs to be rebuilt. It appears something in the mono autogen/configure and/or make clean is not deleting and rebuilding it (or is picking an older libtool vs. actually using glibtool).

I have find that the “libgc/aclocal.m4” has been my main problem:

 ....   
    make[4]: Nothing to be done for `all-am'.
    Making all in doc
    make[3]: Nothing to be done for `all'.
      CC       pthread_support.lo
    libtool: Version mismatch error.  This is libtool 2.4.6, 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
    libtool: and run autoconf again.
    make[3]: *** [pthread_support.lo] Error 63
    make[2]: *** [all-recursive] Error 1
    make[1]: *** [all-recursive] Error 1
    make: *** [all] Error 2

Remove that file:

rm libgc/aclocal.m4 

And re-run the make and it will be recreated correctly.