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

[Leonardo Collado Torres]

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.

Thanks!
Leo