For the "final" step of checking your packages, we recommend the following: R CMD build foo/ R CMD check foo_1.2.3.tar.gz This procedure has the following advantages: 1. Vignette pdfs are generated by the build step and checked in the check step. 2. Running check in this way will not have any side-effects (left behind files) in your package source directory. It is, of course, a bit tedious to build and check. So while you are working on code, you may find it convenient to occasionally run check on the package source directory. Hope that helps clarify things. + seth