[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:
>>
>> 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.

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
"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.

Spencer

>
> Duncan Murdoch
>
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