problem with vignettes when S4 classes in packages overlap
On 12-09-18 7:50 PM, Spencer Graves wrote:
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.
I don't remember for sure, but I don't think your warning or note was the same as Paul's. Generally it's not a good idea to suppress warnings. Someone should fix things so there's no warning. I don't know if that should be RCore because the methods package is issuing a bogus warning, or the maintainer of one of the database packages, or Paul. (From his example, it doesn't look like it should be Paul, unless docs somewhere say that RMySQL and RPostgreSQL can't be used together.) In general, as a package user, I don't want people to be able to suppress checks on CRAN. I want things fixed. So I am pretty sure there won't ever be a reliable "CRAN-detector" put into R. It would devalue the brand. Duncan Murdoch