The option staged.dependencies._storage_dir is being overridden if set by user (i.e. in .Rprofile). When the package is loaded, .onLoad calls setup_storage_dir(path.expand("~/.staged.dependencies")). Then setup_storage_dir takes the given path and sets the option.
On Windows ~/.staged.dependencies can be a OneDrive directory which can cause problems (#169). Regardless, we should not be overriding a user-defined option. We should probably clean up after ourselves as well, resetting any options that we set in the package (i.e. .onUnload())