Such tools are for example scons is a make alternative that rethinks make's
"older timestamp => rebuild"

From www.scons.org/architecture/index.html

*(S)Cons decides if a file was out-of-date by using MD5 checksums of the
> contents of files, not timestamps. *
>


SCons also comes to mind because you are using make for R not (traditional)
programming


*Most of the build tools just mentioned were written by programmers and for
> programmers. The fact that most programmer-friendly utilities do a poor job
> of fulfilling the needs of non-programmers prompted Greg Wilson to organize
> the Software Carpentry competition in January 2000. Software Carpentry was
> an open design contest with the express goal of producing a set of
> next-generation utilities, including a build tool, that would be accessible
> not only to programmers but also to computer **users** such as physical
> scientists. *



[Disclaimer: Ive not tried scons myself]