I am in the process of refining an R package for submission to Bioconductor. My
package has several non-exported functions that include usage examples wrapped
in "dontrun". I do this because these are functions are only called within a
parent function and require complex and esoteric inputs. It would be very
difficult to create dummy inputs that could be generated from a few lines of
preceding code. My only option would be to include inputs as data within the
package, but these would be difficult to describe and would be useful only to
run the example. However, the Bioconductor package guidelines page says "All
man pages should have an runnable examples. donttest and dontrun are
discouraged and generally not allowed" and BiocCheck() complains with notes.
Will a package reviewer fail the submission based on this?
Brian Roberts
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