The Makefile changes are already PR #263. (Further Makefile breakage to use environment variables first is unnecessary — even though bwa has no configure script — as your recipe would use make -e or make CC="$CC" AR="$AR" etc. Cf samtools/samtools#533.)

most build environments export CC without calling make CC="${CC}" explicitly, which just means you need to override the whole default build rule again.

The changes in PR #263 are good, but I'd like to see CC and AR removed, because there is absolutely no need to define them, and removing them breaks nothing.

@jmarshall also, thanks for your kind words on Twitter, pretty rich coming from someone who can't write a build system that builds out of source, or write portable Makefiles, or just plain Autoconf, which you seem to be advocating, yet can't seem to get right yourself (:wave: samtools/htslib@3472494#diff-67e997bcfdac55191033d57a16d1408a).

That htslib commit fixed a minor bug introduced by someone else.

I suggest you keep any discussion here on topic for bwa.

@jmarshall & @SoapGentoo I wonder if Makefile in minimap2 solves the problem. If so, I may change bwa makefile to the minimap2 way.

@lh3 that Makefile is fine as well, as it doesn't explicitly set the CC variable 👍

@lh3 I've dropped the Makefile changes, could you merge the GCC 10 fix?

Thanks.