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

Martin Morgan martin.morgan at roswellpark.org
Thu May 5 12:08:49 CEST 2016

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


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


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 
                      fdef <- get(f, envir = code_env)
-                    if(methods::is(fdef, "genericFunction"))
+                    if(.try_quietly(methods::is(fdef, "genericFunction")))
                          fdef at package == pkgname

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:).


> Thanks!
> Leo
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-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.

More information about the Bioc-devel mailing list