Hello! I made the same mistake is in bug #28002 and got autoconf output like this:
... (some history) checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status .in' Compilation exited abnormally with code 1 at Mon Feb 4 14:18:35 <--- said Emacs Error message ".in" appears confusing. As I think, the original message was (got from config.status output): bash: error: cannot find input file: `XXX/Src/Makefile .in' Could you make multi-line error message fully visible? It was autoreconf (GNU Autoconf) 2.69 running at Linux archlinux 4.20.6-arch1-1-ARCH #1 SMP PREEMPT Thu Jan 31 08:22:01 UTC 2019 x86_64 GNU/Linux Best Regards, Andrey.