I don't like replicating them, either. Not very DRY. Perhaps we can automate updating them when they change in the biom-format examples directory? I'm open to suggestions. 

To answer your question, though, yes, it is recommended to include example data in the package itself since we'll be submitting this to CRAN. On the one hand, I imagine their package check servers are internet-facing and so could instead grab the files directly from the biom-format examples directory. The problem with that solution is that you could then remotely break the R package unit-tests and examples/documentation and have no idea. The success of our package checks on CRAN would then be fragile to GitHub changing the way those files are exposed in a URL (I think this happened at least once, recently), or if you guys change those files for some otherwise perfectly-legitimate reason. You can see the dilemma. My thought was possibly just throwing a warning within the larger biom-format project if the corresponding example files don't match. Then we would know to do something about it and update the corresponding unit-tests at the same time, but without ever putting the current stable release/CRAN version at risk.

Happy to entertain alternatives. This seemed easy, stable, and the files are small.