automake-1.16: error: unrequested trace '$n' Thanks for the report, but it does not happen for me on CentOS 7, using automake-1.16.4. The changes in 1.16.x have been pretty unrelated to autoreconf as far as I can recall, so the cygwin vs. native Unix seems a more likely candidate to me for the culprit, but who knows.
After downloading from https://github.com/crosstool-ng/crosstool-ng, for me running ./bootstrap ends like this: INFO :: *** Running autoreconf configure.ac:96: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from... configure.ac:96: the top level configure.ac:293: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:293: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:293: the top level INFO :: *** Done! I don't think those two "obsolete" warnings (which are coming from autoconf, not automake) are relevant to the problem, but again, who knows. Maybe you or someone else on Cygwin can pursue. --best, karl.