Since this is a warning from a library you didn't write, you can silence warnings from it by enclosing it in a block and turning off warnings in the dynamic scope.
{
local $^W = 0;
call_library_that_warns();
}
Make a very small example that warns- perhaps running a "Hello World" R script- and post a bug report. It could be a bug in either Statistics::R or Win32API::File - but since the example would start with R, then I'd start by reporting there.
If you're ambitious and have time, run that small example script in the debugger shell "perl -d Hello_World_r.pl", and try to find out more about the problem, and perhaps create a patch you can send to the appropriate party...