You can run R non-interactively with input from infile and send output (stdout/stderr) to another file. Here are examples.
# on Linux
R CMD BATCH [options] my_script.R [outfile]
# on Microsoft Windows (adjust the path to R.exe as needed)
"C:\Program Files\R\R-2.13.1\bin\R.exe" CMD BATCH
--vanilla --slave "c:\my projects\my_script.R"
Be sure to look at the section on I/O for help writing R scripts.
See an Introduction to R (Appendix B) for information on the command line options.