I think the problem you are having is with locales. Take notice that you export values with , as decimal separators. I think R is not handling this well.
Please try changing the locale in java before exporting to something like Locale.setDefault(new Locale("en", "NZ"));, make sure the exported values use . for decimals, and try running the script in R.
You do not need to change anything from the R script.
Cheers.