[Bioc-devel] annotation() to BiocGenerics?

[Nicolas Delhomme]

Hi all,

I have the same issue for the easyRNASeq package: 

unable to find an inherited method for function "annotation", for signature "Genome_intervals_stranded"

easyRNASeq uses genomeIntervals (another Bioc package) and due to the mentioned change (moving of the annotation generic), both packages are now partially non-functional.

While I completely support such consolidation, this time, the timeline is very tight. The change was done on the 18th, it took 2 days to propagate, luckily the bug was reported immediately, but it's already friday evening here (21st, CET)  and the API freeze is on the 24th, so if we would play by the rule, there'd just be one day left to fix it (the 24th, can't expect to have someone fixing this at the WE, really). 

This raises a more general concern as there's now really a lot of contributed package in Bioc that depends on the excellent core Bioc API. Would not it make sense to have an earlier freeze of the core Bioc API than just a week before the release? Just to make sure that any effect in downstream contributed packages is timely detected? I'm saying this, because the exact same happened for the 2.10 release 6 months ago. I would not mind sparing that extra bit of stress :-)

I've contacted the maintainer of the genomeIntervals package to see if they can use the BiocGeneric generic instead. 

Robert, it would be good if you were to tell the GSVA developer. And btw, thanks for the tip Benilton!

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Sep 21, 2012, at 12:49 PM, Robert Castelo 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]]
>>>> 
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>>> 
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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
> 
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