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

Leonardo Collado Torres lcollado at jhu.edu
Thu May 5 08:05:45 CEST 2016


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

I've read a few times
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


More information about the Bioc-devel mailing list