[BioC] error with ontoCompare (goTools)

[Wolfgang Raffelsberger]

Dear list,
I'm interested in making a graph (pie-chart or similar) showing the 
different GO ontologies one may get from a list of genes (in my case a 
list of Affymetrix probe-sets).  In this context it might be good only 
to compare a given level of GO-ontologies (to avoid redundancies with 
terms closer to the root), ideally I'd like use something close to GO-slim.

It looks like that goTools allows to do something close to what I'm 
interested (without the GOslim...).
So I tried to use goTools but running the code from the documentation 
(as suggested in ?ontoCompare ) I got the following error :

library(goTools)
library(GO.db)
data(probeID)
 affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- affylist[[2]][1:4])   
# shorter list just for testing ...
 res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T)

and I get the following (error) message :

Starting ontoCompare...
Error in FUN(X[[1L]], ...) :
  unused argument(s) (list(`GO:0000001` = <S4 object of class 
"GOTerms">, `GO:0000002` = <S4 object of class "GOTerms">, `GO:0000003` 
= <S4 object of class "GOTerms">, `GO:0000006` = <S4 object of class 
"GOTerms">, `GO:0000007` = <S4 object of class "GOTerms">, `GO:0000009` 
= <S4 object of class ...

Am I missing somthing ?
Other suggestions ?

Thank's for any hints,
Wolfgang


Just for completeness:
sessionInfo()

R version 2.8.1 (2008-12-22)
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] tools     stats     graphics  grDevices datasets  tcltk     
utils     methods   base    

other attached packages:
 [1] hgu133a.db_2.2.5    annotate_1.20.1     xtable_1.5-4        
goTools_1.16.0      GO.db_2.2.5       
 [6] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.4.2 
Biobase_2.2.1       svSocket_0.9-5    
[11] svIO_0.9-5          R2HTML_1.59         svMisc_0.9-5        
svIDE_0.9-5   


 
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
CNRS UMR7104, IGBMC 
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr