Awesome, thanks Martin! You make it look easy!
On Thu, May 5, 2016 at 6:08 AM, Martin Morgan <martin.mor...@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@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 >> >> _______________________________________________ >> Bioc-devel@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. > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
