Mmm, if you did set your relative path properly, shouldn't you be shown
"Error in setwd("../../export_stats_files/") : cannot change working directory. Execution halted''
Can you add a few
getwd() along your script, to ensure what is the working directory at the begining and at the end of your R call?
As far as I remember, you were only calling your relative path at the beginning of your R script, so seting the wd properly at the beginning should fix it.