Yes that was the problem, cygwin is no longer in my
system, but it was a ".profile" file in my home dir.
Maybe you have already set the HOME environment
variable before starting MSYS, and maybe that directory contains a ".profile"
or a similar file? That would not be a problem in itself, but you would need
to make sure the script doesn't try to use any commands (like whoami) that
don't exist in MSYS. If the existing script is for Cygwin you could use the
output of "uname" in the script to check whether MSYS or Cygwin is running.
And again, you need to make sure Cygwin is not in your PATH while running