[Rd] problem with vignettes when S4 classes in packages overlap

Spencer Graves spencer.graves at prodsyse.com
Wed Sep 19 01:50:30 CEST 2012

On 9/18/2012 4:23 PM, Duncan Murdoch wrote:
> On 12-09-18 5:40 PM, Paul Gilbert wrote:
>> ( A similar problem is also reported by Sebastian P. Luque with
>>     library(maptools)
>>     library(trip)
>> in the vignette as below ).
>> I am writing a vignette which loads RMySQL and RPostgreSQL. This
>> produces the warning:
>> Loading required package: DBI
>> Warning in .simpleDuplicateClass(def, prev) :
>>     A specification for class “dbObjectId” in package ‘RPostgreSQL’ 
>> seems
>> equivalent to one from package ‘RMySQL’ and is not turning on duplicate
>> class definitions for this class
>> This can be reproduced by running
>>     R CMD Sweave --pdf Atest.Stex
>> where the file Atest.Stex has the lines
>> \documentclass{article}
>> \usepackage{Sweave}
>> \begin{document}
>> \begin{Scode}
>> library("RMySQL")
>> library("RPostgreSQL")
>> \end{Scode}
>> \end{document}
>> These warnings only happen in a vignette. They are not produced if the
>> lines are entered in an R session.
>> (Using R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" on Ubunt
> You'll get the warning in a regular session if you set 
> options(warn=1).  I think Sweave is probably doing this so that 
> warnings show up around the time of the chunk they correspond to. It 
> does it in the command line version, but not in the Sweave() function 
> (which would save them up to the end).
> I don't know if the warning is something you should worry about or not.

       On August 30, 2012, CRAN maintainers rejected the latest version 
of "fda", and I understood them to say it was rejected because the 
current CRAN policy did not accept packages reporting either "Notes" or 
"Warnings".  As part of my efforts to comply with this, I started the 
thread on [Rd] subject:  "if(--as-cran)?"  I added a function "CRAN" to 
"fda", and I thought someone had added a more general function to the 
development version of R. Unfortunately, I can't find documentation of 
that more general function now.


> Duncan Murdoch
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