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).

make clean is the way to go; here to add some further words of clarification on what's going on.

You attempted to build R with the wrong options (i.e., without using --enable-R-shlib as is required to use it with RStudio), and in the process did either a full or a partial build of R.

Your error message says the issue arose in ./src/main, where the earlier make compiled the .c files there into the .o files. When you re-run make after re-./configure-ing with the right options, it sees those .o files and says "I don't need to re-compile the .c files here, .o files already exist" and attempts to proceed.

However, those .o files were compiled under a different configuration, so they are "stale" in that sense -- make clean removes those .o files (as well as any other artefacts of the earlier build that are now obsolete).

There may be a more minimal way of resetting your build (make clean removes all built files from the earlier make, but maybe only some subset of those is required), but this would probably depend on what exactly is the difference between the earlier ./configure options and the new ones, and you're apt to spend more time tinkering than it would take to just do a clean build (personally, I gave up after removing all the ./src/main/*.o files wasn't enough).