R loads files in alphabetical order. Unfortunately not every alphabet puts letters in the same order, so you can't rely on alphabetic ordering if you need one file loaded before another. The order in which files are loaded doesn't matter for most packages. But if you're using S4, you'll need to make sure that classes are loaded before subclasses and generics are defined before methods.
Rather than relying on alphabetic ordering, roxygen2 provides an explicit way of saying that one file must be loaded before another: @include. The @include tag gives a space separated list of file names that should be loaded before the current file:
#' @include class-a.r
setClass("B", contains = "A")
If any @include tags are present in the package, roxygen2 will set the Collate field in the DESCRIPTION, which ensures that files are always loaded in the same order.