Renaud Lancelot
2007-Apr-01 09:54 UTC
[Rd] 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
Prof Brian Ripley
2007-Apr-01 10:32 UTC
[Rd] new warnings related to the extractor "$" with R 2.5.0alpha
On Sun, 1 Apr 2007, Renaud Lancelot wrote:> Dear all, > > I just installed R 2.5.0alpha and noticed new warnings related to the > extractor "$" 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