From murdoch.duncan at gmail.com  Wed Sep 19 01:23:47 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 18 Sep 2012 19:23:47 -0400
Subject: [Rd] problem with vignettes when S4 classes in packages overlap
In-Reply-To: <5058EA54.8050305@gmail.com>
References: <5058EA54.8050305@gmail.com>
Message-ID: <50590283.4030700@gmail.com>

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.

Duncan Murdoch



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