[Bioc-devel] annotation() to BiocGenerics?

[Benilton Carvalho]

Replace

Biobase::`annotation<-`(eScoEset, "")

by

Biobase::`annotation<-`(eScoEset, value="")

b

On 21 September 2012 11:49, Robert Castelo <robert.castelo at upf.edu> wrote:
> 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
>>>
>>>
>>> _______________________________________________
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>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> 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
>
>
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