@harlantc, in general, please open new issues for new problems. That said, I took a quick look at the build.log you provided and it was not obvious exactly why things went wrong. The most obvious difference is that when I do a 3.9.4 build, the extension module source paths (the -c arguments to the failing compiles) have been normalized by setup.py to absolute paths, whereas in the failing build.log they are unprefixed relative paths. I suggest you look at the top level setup.py file to figure out why that is the case in your build. I also note that the build appears to be on a very early release of macOS 11 Big Sur; it would be best to upgrade to the latest version of it and ensure you have the latest version of the Command Line Tools installed. Also, your configure arguments appear to be unnecessary complex: the -m64 and the --build and --target arguments shouldn't be necessary and we rarely test with --enable-shared on macOS. It's possible they are contributing factors.  If you do find something that appears to be a Python build issue, please open a new issue with the details.