[Bioc-devel] Use of dontest in function documentation

[Kern, Lori]

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-bounces using r-project.org> on behalf of Brian Roberts via Bioc-devel <bioc-devel using r-project.org>
Sent: Friday, December 8, 2023 3:08 PM
To: bioc-devel using r-project.org <bioc-devel using 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
        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1cwm_fDuiZ1AyyAjvbfmzapP5BnMFSI9KdmkvCt-CDq3GUCv5sFvgREysbQ_8I01cFIxBcAYEpIMLugdltmsx8IA2Pu5Z3yJ0jZ2gCGc2hUikkx7hHY8Hjx1hUoIKmUJ1BpbSBTvb4m8jOhu0Nq9NmjDMc6V2qILDHfKyKx9NFL6C3CSW3fAU_a1UNuJPPbKKLEbTWI2C8oaVqpIyLJ8rxpOYaTFPwHDCTOlC0SJOdC_NKlzkVRhFpk5W2ZRB0a1IXdxuOWjXlKKyrZMQ-3UPeN2ISzbFLHOSckkVN6SflFAAQx4OmXAtpkove7J61kYp/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]