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

[L Rutter]

Hi Lori and Kevin:

Thank you for your helpful responses! I was able to use "if
(interactive()) { ... }" format and return the appDir object for the
user. Thanks again!

Lindsay
On Mon, Nov 19, 2018 at 3:02 PM Kevin RUE <kevinrue67 using gmail.com> wrote:
>
> Hi Lindsay,
>
> Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R function "iSEE" for an example of both the function return value, and the man page.
>
> First, I would suggest that your function _returns_ the "appDir" object to the user, and that you leave it to the user to call "shiny::runApp" with options appropriate to their system or preferences (e.g launch.browser=FALSE, port=1234, etc).
>
> Second, for the man page, you don't have to put the _entire_ @example block inside \dontrun{}. You can put everything that doesn't launch the Shiny app outside the \dontrun{} block and only put the one "shiny" line inside the \dontrun{}. The one line will represent less than 80% of the man page.
>
> However, even better, you can avoid the \dontrun{} option altogether and put the "shiny" statement within a "if (interactive()) { ... }" block.
>
> So adapting you existing code, I would have
> #' @examples
> #' # Example 1: Create an interactive litre plot for the logged data using
> #' # default background of hexagons.
> #'
> #' data(soybean_ir_sub)
> #' data(soybean_ir_sub_metrics)
> #' soybean_ir_sub_log <- soybean_ir_sub
> #' soybean_ir_sub_log[,-1] <- log(soybean_ir_sub[,-1]+1)
> #' if (interactive()){
> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = soybean_ir_sub_metrics)
> #' }
> #'
> #' # Example 2: Repeat the same process, only now plot background data as
> #' # individual points. Note this may be too slow now that all points are drawn
> #' # in the background.
> #' if (interactive()){
> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = soybean_ir_sub_metrics,
> #' option = "allPoints", pointColor = "red")
> #' }
>
> However, once more, I suggest that you return "appDir", and you would then have something like:
> #' app <- plotLitreApp(data = soybean_ir_sub_log, dataMetrics = soybean_ir_sub_metrics)
> #' if (interactive()){
> #'    shiny::runApp(app, [options defined by your user])
> #' }
>
> I hope this helps. Otherwise, let me know and I can chime in the review of your package
>
> Best wishes
> Kevin
>
> On Mon, Nov 19, 2018 at 7:00 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org> wrote:
>>
>> 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
>> 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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