[Bioc-devel] R CMD check error related to data docs in a new package

[Leonardo Collado Torres]

Awesome, thanks Martin!

You make it look easy!

On Thu, May 5, 2016 at 6:08 AM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:
>
>
> On 05/05/2016 02:05 AM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> I need some help with a new package I'm coding (which we plan to
>> submit to BioC). I keep getting a warning in R CMD check that I
>> haven't been able to figure out what is wrong. I'm guessing that it's
>> something fairly straightforward, I'm just not seeing it right now.
>>
>> The warning is:
>>
>> checking for missing documentation entries ... WARNING
>> ## some output from loading SummarizedExperiment
>> All user-level objects in a package should have documentation entries.
>> See chapter ‘Writing R documentation files’ in the ‘Writing R
>>
>> See https://travis-ci.org/leekgroup/recount/builds/127982505#L746-L778
>> for details. The package code that matches this build report is
>>
>> https://github.com/leekgroup/recount/tree/35c0f786411e8e63b9ed76866d71273fef9654ea.
>>
>> I've read a few times
>>
>> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-data-sets
>> and double checked the documents. They seem fine to me.
>>
>> My guesses are:
>> * Maybe I need to add to imports the SummarizedExperiment package,
>> although the links like
>> \link[SummarizedExperiment]{RangedSummarizedExperiment-class} do work.
>> * Maybe I need to add \source{...} although I don't see this warning
>> with
>> https://github.com/lcolladotor/derfinder/blob/master/R/genomicState-data.R
>> which doesn't use \source{...}
>>
>> If you have any tips on how I could narrow down the warning, that'd be
>> great. I guess that I can try removing 1 by 1 the 5 data objects from
>> this new package, building and checking to find which of them is the
>> culprit.
>
>
> You can reproduce this problem by installing recount and saying
>
>     tools::undoc("recount")
>
> The output from loading packages is unexpected.
>
> The problem occurs when tools::undoc() tries to check that the data objects
> are documented. When an S4 object is loaded, at
>
>   https://github.com/wch/r-source/blob/trunk/src/library/tools/R/QC.R#L189
>
> This triggers loading of packages defining any classes in the object. In
> your case I guess you have a SummarizedExperiment, and so the
> SummarizedExperiment package is loaded. The output from loading the package
> is interpreted as a warning message.
>
> I think a fix for R-3-3-branch is
>
> Index: src/library/tools/R/QC.R
> ===================================================================
> --- src/library/tools/R/QC.R    (revision 70582)
> +++ src/library/tools/R/QC.R    (working copy)
> @@ -186,7 +186,7 @@
>                  Filter(function(f) {
>                      ## NB: this get() is expensive as it loads every object
>                      fdef <- get(f, envir = code_env)
> -                    if(methods::is(fdef, "genericFunction"))
> +                    if(.try_quietly(methods::is(fdef, "genericFunction")))
>                          fdef at package == pkgname
>                      else
>                          TRUE
>
> I think you should live with the warning, counting on this fix to be
> applied, rather than come up with a workaround (moving SummarizedExperiment
> from Suggests: to Depends:).
>
> Martin
>
>>
>> Thanks!
>> Leo
>>
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>>
>
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