Is there a way to compile only some *.c (or *.cpp) files in src folder and not all of them? Perhaps it may be possible by modifying Makevars somehow?
A bit of background: I made a mistake of committing some files to the git master branch and would be easier for me to avoid their compilation rather than renaming them all or removing the branch.
That really is a Makefile (language) question that you can address via a Makevars file with proper settings.
But beware:
R really prefers the default settings and its implicit Makefile. You can get by with Makevars for settings things like compiler / linker options, doing dependencies among files right is much harder. Very few packages do it right. You are more likely to break dual-architecture builds on, eg, OS X and (via Makevars.win) on Windows.
There is no reason to leave the repo in a sad state. Just clean up your git repo, and the world will be a better place too.