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Additional note, since I forgot it in the initial message: I'm building Python 3.9.0 from source on Debian v10, specifically the Debian VM on Chromebooks (which I believe is called Crostini).
I've made sure to install all the proper dependencies, as far as I know, and I'm 99% sure that I can successfully build it if I remove the --with-memory-sanitizer flag. Running the command again without it to double-check.
Yeah, exactly as I thought, ran the exact same command except without --with-memory-sanitizer and the configuration was successful. The successful output has been attached in configure-out-1.txt for cross-comparison, if it's necessary.
The --with-memory-sanitizer option adds "-fsanitize=memory -fsanitize-memory-track-origins=2 -fno-omit-frame-pointer" to CFLAGS, and "-fsanitize=memory -fsanitize-memory-track-origins=2" to LDFLAGS. The MemorySanitizer is a clang specific feature, AFAIK. You're using GCC, so what happens is that these (GCC incompatible) flags are added and the following compile check (getaddrinfo) fails.
IMO, adding a compiler check and printing a warning if --with-memory-sanitizer is used with GCC should be an ok solution. Alternatively, we inform the user that we're switching to using the leak sanitiser, if we're on GCC.