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-boun...@r-project.org> on behalf of L Rutter
<lindsayannerut...@gmail.com>
Sent: Monday, November 19, 2018 1:49:50 PM
To: bioc-devel@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
resolve:
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
format:
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:
https://github.com/lrutter/bigPint/blob/master/R/plotLitreApp.R
Thank you for any advice!
Lindsay
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