From renaud.lancelot at gmail.com  Sun Apr  1 13:17:27 2007
From: renaud.lancelot at gmail.com (Renaud Lancelot)
Date: Sun, 1 Apr 2007 13:17:27 +0200
Subject: [Rd] new warnings related to the extractor "$" with R 2.5.0alpha
In-Reply-To: <Pine.LNX.4.64.0704011119390.14756@gannet.stats.ox.ac.uk>
References: <c2ee56800704010254w68c4f5b5ke51a7aca1e4a93ed@mail.gmail.com>
	<Pine.LNX.4.64.0704011119390.14756@gannet.stats.ox.ac.uk>
Message-ID: <c2ee56800704010417g57087b85s4997f947070b9b86@mail.gmail.com>

Thank you for this explanation. As the package maintainer for aod
(second warning message), I found where the warning came from and will
post an update soon.

Kind regards,

Renaud

2007/4/1, Prof Brian Ripley <ripley at stats.ox.ac.uk>:
> On Sun, 1 Apr 2007, Renaud Lancelot wrote:
>
> > Dear all,
> >
> > I just installed R 2.5.0alpha and noticed new warnings related to the
> > extractor "$" when using contributed packages. For instance:
> >
> >> library(RODBC)
> > Warning message:
> > $ operator is not valid for atomic vectors, returning NULL
> >
> >> library(aod)
> > Package aod, version 1.1-18
> >> data(orob2)
> >> m1 <- betabin(cbind(y, n-y) ~ 1, random = ~ 1, data = orob2)
> >> head(residuals(m1))
> >         1          2          3          4          5          6
> > -1.4629774 -0.7897877 -1.3754283  0.1029910 -0.3556985  1.4030026
> > Warning message:
> > $ operator not defined for this S4 class, returning NULL
> >
> > In these two cases, I deleted the former installations and re-built
> > the packages from sources.
> >
> > How to overcome this problem ?
>
> Wait for package updates.  For RODBC, it is harmless but the warning will
> not appear in 1.1-9 (which will be released before R 2.5.0 is).
>
> (The first message is not really right: $ for lists was valid and
> documented to return NULL in released versions of R, as it was in the Blue
> Book.  It should say that it is 'deprecated' in R 2.5.0, since this
> amounts to a change of language definition and that should be giving a
> warning of deprecation.)
>
> Later versions of R 2.5.0 alpha give more informative messages.
>
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>


-- 
Renaud LANCELOT
D?partement Syst?mes Biologiques du CIRAD
CIRAD, Biological Systems Department

Campus International de Baillarguet
TA 30 / B
F34398 Montpellier
Tel   +33 (0)4 67 59 37 17
Secr. +33 (0)4 67 59 37 37
Fax   +33 (0)4 67 59 37 95



[Rd] new warnings related to the extractor "$" with R 2.5.0alpha
Renaud Lancelot