[Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Mon Nov 19 19:55:18 CET 2018

Submit with the dontrun{} and temporarily ignore the ERROR -  when submitting please reference the explanation below.  Your reviewer could provide more information and will decide how to proceed -  generally examples will be run manually to check for accuracy and an exception can be made.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of L Rutter <lindsayannerutter using gmail.com>
Sent: Monday, November 19, 2018 1:49:50 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

Hello all:

I am planning to submit a package to Bioconductor and have one last
item from BiocCheck (error, warning, note) I have been unable to

ERROR: At least 80% of man pages documenting exported objects must
have runnable examples. The following pages do not: plotLitreApp.Rd,
plotPCPApp.Rd, plotSMApp.Rd, plotVolcanoApp.Rd

I have 18 man pages (9 function-related, 8 data-related, and 1
package-related). Of these, 4 of the function-related man pages (the
ones listed in the ERROR) are Shiny applications of the following

appDir <- system.file("shiny-examples", "plotLitreApp", package = "bigPint")
shiny::runApp(appDir, display.mode = "normal")

If I do not have \dontrun{} around these shiny app examples, then R
CMD check permanently halts on the "checking examples..." step. If I
do have \dontrun{} around these shiny app examples, then R CMD
BiocCheck gives me the error above. My question is: What is the
recommended procedure in such a situation where the package is being
prepared for Bioconductor submission?

An example of one script causing the error can be found at:

Thank you for any advice!

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