OK, it does look like there are issues with recent versions of MSYS2, as reported in this post and this one… Can I ask you to try the following:
-
bring your MSYS2 installation up to date (instructions here)
-
bring your MRtrix3 installation up to date:
$ git checkout master $ git pull -
try running
configure&buildusing the MSYS2 version ofpython(rather than the MinGW version):$ /usr/bin/python ./configure $ /usr/bin/python ./build
If that still doesn’t work, please post your configure.log file - it might give us a hint as to where the problem might be…