[Bioc-devel] annotation() to BiocGenerics?

Fri Sep 21 18:07:12 CEST 2012

On 09/21/2012 08:37 AM, Nicolas Delhomme wrote:
> 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"

this doesn't show up in the build report? How can it be reproduced?

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

we'll clean up our mess, but thanks for the report.

> 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 :-)

Sorry for the inconvenience; we do try to avoid things that will 
definitely be disruptive.

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

genomeIntervals should previously have importFrom(Biobase, annotation, 
"annotation<-") in its NAMESPACE.

Martin

>
> 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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>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>> _______________________________________________
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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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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