[Bioc-devel] Questions about some checks in the latest BiocCheck

Casper Peters cp100u @ending from hotm@il@com
Wed Nov 28 16:34:17 CET 2018

So in the package I'm developing, I have a few specific use cases that make BiocCheck not so happy.



* WARNING: Avoid class()== or class()!= ; use is() or !is()


So my first problem arises with checking the classes of objects. I want the interface to be such that I can allow for case insensitivity and/or allow the object to be NULL in some specific cases. This is easier with using `class()` explicitly (especially in the case of case sensitivity).



 * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples. The following pages do not:

The second problem arises because of some of my exported functions. I made parser+download functions for the Fantom5 data, as this was not available anywhere inside a package yet. Because of the download being big/taking too long, I want to avoid running the checks in R CMD check. For this I added \dontrun{} at the examples, resulting in BiocCheck not liking this.

Other than that I just have some small notes that I still need to take care of, but with these I am not sure what to do.

Thanks in advance,


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