JonY wrote:

>
>  MSYS has been strongly associated with mingw.org for a very long
>  time, hence to autotools, MSYS uname string can be assumed to be
>  i686-pc-mingw32.
>

Let me state that the string from the MSYS uname is controlled by an 
environment variable MSYSTEM.  So if MSYSTEM is changed to say mingw64 
then the config.guess and config.sub scripts could be changed to 
recognize the uname string to produce i686-pc-mingw64, x86_64-mingw64 or 
even x86_64-w64-mingw32 which ever is preferred.  The uname string from 
MSYS would read MINGW64_NT-5.1 if MSYSTEM=mingw64.

My personal preference for a config.guess return string would be 
x86_64-w64-mingw.

--
Earnie

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