How to configure R-3.1.2 with --enable-R-shlib

make uninstall only undoes the make install step, which generally copies the files from the compilation dir to dir(s) on the system as appropriate, and puts binaries in say /usr/bin so they are on the path. If you wanted to clean up the dir where you did a previous compile, use make clean (or make distclean, I forget what the difference is now as far as R is concerned but convention is that it should return the build dir to pre-configure, pre-build state.).

You also, in general, don't want to be building in the dir which contains the R sources (which ./configure suggests you are doing).