[BioC] goTools package, ontoCompare error

[Craig Johnson]

Dear list,

If someone could please help me figure out what I am missing I would be very grateful. My error can be recreated using the package data set and example and only occurs when using custom end nodes. The code and session info follow. 

Thanks,
Craig 

> library("goTools", verbose=FALSE)
> library("GO.db")
> data(probeID) 
> subset=c(L1=list(affylist[[1]][1:5]),L2=list(affylist[[2]][1:5]))
>  MFendnode <- CustomEndNodeList("GO:0003674", rank=2)
rank= 1 
rank= 2
>  res <- ontoCompare(subset, probeType="hgu133a", endnode=MFendnode, goType="MF")
Starting ontoCompare...
Loading required package: org.Hs.eg.db
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "Ontology", for signature "NULL"


> traceback()
7: stop("unable to find an inherited method for function \"", fdef at generic, 
       "\", for signature ", cnames)
6: function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste("\"", sapply(classes, as.character), 
               "\"", sep = "", collapse = ", ")
           stop("unable to find an inherited method for function \"", 
               fdef at generic, "\", for signature ", cnames)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method")
   }(list("NULL"), function (object) 
   standardGeneric("Ontology"), <environment>)
5: FUN(X[[1L]], ...)
4: lapply(X, FUN, ...)
3: sapply(FullGOenv[index], Ontology)
2: getOntology(endnode, goType, FullGOenv)
1: ontoCompare(subset, probeType = "hgu133a", endnode = MFendnode, 
       goType = "MF")



> sessionInfo()
R version 2.10.0 (2009-10-26) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods  
[8] base     

other attached packages:
 [1] hgu133a.db_2.3.5    org.Hs.eg.db_2.3.6  goTools_1.20.0     
 [4] GO.db_2.3.5         RSQLite_0.7-3       DBI_0.2-4          
 [7] AnnotationDbi_1.8.0 genefilter_1.28.0   Biobase_2.6.0      
[10] limma_3.2.1        

loaded via a namespace (and not attached):
[1] annotate_1.24.0 splines_2.10.0  survival_2.35-7 xtable_1.5-5   


Craig Johnson
Biostatistician, UM Microarray Core
7410 CCGC
1500 E. Medical Center Dr.
Ann Arbor, MI 48109-0946


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