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See in particular: http://stackoverflow.com/questions/13575353/how-does-the-shiny-r-package-deal-with-data-frames Also reported at different times by Dirk Eddelbuettel and Jay Emerson. The observed behavior is that S3/S4 method dispatch does not always seem to work; the desired methods are not invoked despite appearing to be in the search path. The problem was that sourcing files with local=TRUE creates a new environment based on the parent frame, which in our case is Shiny's package environment. What we really want is to read from the global environment but write to a throwaway environment. The correct way to do that is to make a new environment with .GlobalEnv as the parent.