Not if its justified but I'd be sure to mark the man pages as internal (if
using roxygen you can do @keywords internal) . Normally that is referring to
any exported function. I assume adequate testing, or examples in exported
functions are run?
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Brian Roberts
via Bioc-devel <bioc-devel@r-project.org>
Sent: Friday, December 8, 2023 3:08 PM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] Use of dontest in function documentation
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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