I am using R on a Unix system. I wrote an R script in windows, and uploaded it to Unix (via putty), such that I could run the script in R (in unix) with the command
write.table(myDataOutput, file = "/myfolder/wantedData.txt")
I have had this problem myself, not being able to figure out the default directory which R uses for a file with a relative path. Since you used an absolute path, the file should be found at
\myfolder\wantedData.txt. If it isn't there, you can try searching for it:
sudo find . -name 'wantedData.txt`
If this search comes up empty, then R did not write the file. If you find it, but in a location which you did not expect, then most likely R interpreted your path as a relative, rather than absolute, path. In this case, remember the location so you can find your file next time.
Based on the warning message you got from Unix, I would guess that your R script does not have permissions to write the output file in the location you specified. You could try running the R script with
sudo, which might get around this problem.