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A general description is here.
LaTeX package ‘upquote’ is no longer required for R's use of ‘inconsolata’.
The ‘\donttest’ sections of R's help files can be tested by ‘make check TEST_DONTTEST=TRUE’.
‘R CMD Sweave’ no longer cleans any files by default, compatibly with versions of R prior to 3.1.0. There are new options ‘--clean’, ‘--clean=default’ and ‘--clean=keepOuts’.
There is more extensive advice on which LaTeX packages are required to install R or to make package manuals (as done by ‘R CMD check’, in the ‘Writing R Extensions’ manual.