[Bioc-devel] annotation() to BiocGenerics?

[Robert Castelo]

Dear Valerie and other developers,

executing the vignette from package GSVA fails with an error related to 
the change described in your email (because before it did not appear):

Error: processing vignette ‘GSVA.Rnw’ failed with diagnostics:
  chunk 19
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function "annotation<-", for 
signature "ExpressionSet", "missing"
Execution halted

the main function of the package, gsva(), calls at some point 
'annotation(eset)' for some ExpressionSet object 'eset'.

i've tried the following solutions:

1. put in NAMESPACE

importFrom(Biobase, annotation)

and replace every call to 'annotation()' by 'Biobase::annotation()'

2. put in NAMESPACE

importFrom(BiocGenerics, annotation)

and replace every call to 'annotation()' by 'BiocGenerics::annotation()'


but none of them work, both give still the same error.

i've executed the vignette interactively and this is the traceback() and 
sessionInfo() at the line of code producing the error:

 > gbm_es <- gsva(gbm_eset, brainTxDbSets, mx.diff=FALSE, 
verbose=FALSE)$es.obs
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function "annotation<-", for 
signature "ExpressionSet", "missing"
 > traceback()
6: stop("unable to find an inherited method for function \"", fdef at generic,
        "\", for signature ", cnames)
5: function (classes, fdef, mtable)
    {
        methods <- .findInheritedMethods(classes, fdef, mtable)
        if (length(methods) == 1L)
            return(methods[[1L]])
        else if (length(methods) == 0L) {
            cnames <- paste0("\"", sapply(classes, as.character),
                "\"", 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("ExpressionSet", "missing"), function (object, ..., value)
    standardGeneric("annotation<-"), <environment>)
4: Biobase::`annotation<-`(eScoEset, "")
3: .local(expr, gset.idx.list, annotation, ...)
2: gsva(gbm_eset, brainTxDbSets, mx.diff = FALSE, verbose = FALSE)
1: gsva(gbm_eset, brainTxDbSets, mx.diff = FALSE, verbose = FALSE)

whose interpretation goes beyond my expertise, so i hope somebody more 
experienced than me has a hint about the problem :)

cheers,
robert.

On 09/18/2012 08:48 PM, Valerie Obenchain wrote:
> 'annotation' and 'annotation<-' have been moved from Biobase (2.17.8) to
> BiocGenerics (0.3.2). This should propagate through tomorrows build.
>
> Valerie
>
>
> On 08/30/2012 11:35 AM, Valerie Obenchain wrote:
>> Hi Vince,
>>
>> Yes we can add this to BiocGenerics. I'll post back when it's done.
>>
>> Valerie
>>
>>
>> On 08/29/2012 07:25 AM, Vincent Carey wrote:
>>> currently in Biobase
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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>
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-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550