this sounds like a silly problem: I'm putting my R code into a package and R CMD check src complains about the .Rd~ backup files being produced by Emacs.
* checking package subdirectories ... WARNING
Subdirectory 'man' contains invalid file names:
read.PI.Rd~ write.PI.Rd~
the documentation says: »In addition [...] files [...] with base names [...] ending in ‘~’, ‘.bak’ or ‘.swp’, are excluded by default.« (page 18). but then why the warning?
Just add a file cleanup which removes them in your top-level directory. Also, you could build a tarball or zip archive first via R CMD build and the check this archive via R CMD check -- that should skip these filese as well.
Also, exactly how are you calling R CMD check, and what is your directory layout? With R 2.10.0 on Linux, I just ran touch pkg/man/foo.Rd~ for one of my packages, and R CMD check pkg (where pkg is the top-level directory as common for source projects stored on R-Forge)
did not issue this warning you are seeing. The file was not removed by cleanup as that currently purges only in src.