I also had this problem thanks to the restrictions on writing to /usr in El Capitan. Redownloading R and MacTex does solve the problem, as mentioned in another answer, but you can avoid re-downloading MacTex by entering this into terminal:
sudo ln -s Distributions/Programs/texbin texbin
echo "/Library/TeX/texbin" >~/Desktop/TeX
sudo cp ~/Desktop/TeX /etc/paths.d/TeX
Rscript is off limits now though, thanks to the changes. Try checking in Terminal:
which Rscript. I had to re-download R though, which worked. Now when I do
which Rscript I get:
Alternatively, try running in Rstudio, which accesses R directly.