incomplete line in the rprofile.site

Question

When I send command from Tinn-R to R by hotkey, sometimes this error shows up:

Error in source(.trPaths[5], echo = TRUE, max.deparse.length = 150) : 
  object '.trPaths' not found

But If I copy and paste the same command into R manually, no error message at all.

Then I tried:

> grep(".trPaths",readLines(file.path(R.home(component="etc"),"Rprofile.site")))>0

and the message was:

In readLines(file.path(R.home(component = "etc"), "Rprofile.site")) :
  incomplete final line found on 'D:/Programs/R-3.1.1/etc/Rprofile.site'

I did make a change to the rprofile.site by adding a line setting up my working directory.

Any suggestion what I should do?

Thanks.