[Bioc-devel] annotation() to BiocGenerics?

[Martin Morgan]

On 09/21/2012 05:05 AM, Benilton Carvalho wrote:
> Replace
>
> Biobase::`annotation<-`(eScoEset, "")
>
> by
>
> Biobase::`annotation<-`(eScoEset, value="")

why not just

    annotation(eScoEset) <- ""

with importFrom(Biobase, "annotation<-") in the NAMESPACE?

Martin

>
> 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
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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
>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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