R devel - Apr 2007 - new warnings related to the extractor "$" with R 2.5.0alpha

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 ?

Kind regards,

Renaud

##################
> sessionInfo()
R version 2.5.0 alpha (2007-03-30 r40957)
i386-pc-mingw32

locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

attached base packages:
[1] "stats"     "graphics"  "grDevices"
"utils"     "datasets"
"tcltk"     "methods"   "base"

other attached packages:
     aod    RODBC fortunes     svIO   R2HTML   svMisc svSocket    svIDE
"1.1-18"  "1.1-8"  "1.3-2"  "0.9-5"  
"1.58"  "0.9-5"  "0.9-5"  "0.9-5"



-- 
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

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