R devel - Sep 2012 - problem with vignettes when S4 classes in packages overlap

( 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
Ubuntu)

Paul

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

On Tue, 18 Sep 2012, Paul Gilbert wrote:
>
> ( A similar problem is also reported by Sebastian P. Luque with
>  library(maptools)
>  library(trip)
> in the vignette as below ).
Thanks for bringing this up. This is caused by maptools avoiding: Depends: 
spatstat, which might create circularities. maptools and spatstat (which 
defines the classes that maptools and trip augment by adding coercion to 
and from their own or sp classes) mutually Suggest: each other. trip 
Depends: spatstat, but out of the box has no NAMESPACE - I haven't 
investigated whether adding one helps.

Adding maptools to trip::Depends removes the warnings; check passes as 
before, so no side-effects I can see. The auto-generated NAMESPACE is 
then:

# Default NAMESPACE created by R
# Remove the previous line if you edit this file

# Export all names
exportPattern(".")

# Import all packages listed as Imports or Depends
import(
   methods,
   sp,
   spatstat,
   maptools
)

Since trip was last updated in May 2011, it is missing both a NAMESPACE 
file, and suggestion of the correct adehabitat?? package(s) - adehabitat 
is deprecated. I don't think that this is an S4 problem, I think it is 
about keeping packages in sync with the R engine, especially with regard 
to NAMESPACE, etc., and with packages named in DESCRIPTION. This may carry 
over to the main case here, but I haven't checked.

Roger
>
> 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
Ubuntu)
>
> Paul
>
-- 
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no