[Bioc-devel] Biobase/IRanges annotation maksing

[Wolfgang Huber]

Hi

of course there is no fundamental reason why the same name should not be 
used for different things in different packages, and in many instances 
this is the most reasonable solution. However, I think the 
user-friendliness of the set of Bioconductor packages would be improved 
if authors tried to keep such instances to a minimum.

Since there is considerable overlap and collaboration between the 
authors of Biobase and IRange I am optimistic that a (perhaps less 
modular but) more integrated solution could be found.

Currently, the generic function Biobase::annotation has exactly one 
method, for signature "eSet", and the generic function 
IRanges::annotation has exactly one method, for signature 
"AnnotatedList". I.e. although they are generic functions in the 
S4-technical sense, neither is generic in the common sense of the word. 
I think it could be a goal for us that the concepts "S4" and "common 
sense" be not opposed to each other.

Best wishes
      Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Martin Morgan wrote:
> Laurent Gatto <l.gatto at dnavision.be> writes:
> 
>> Dear Bioc developeRs,
>>
>> I noted recently that Biobase's 'annotation' and 'annotation<-' objects are 
>> masked by IRanges. Now calling annotation(AffyBatch), of 
>> annotation(ExpressionSet) throws an 'unable to find an inherited method for 
>> function "annotation", for signature "AffyBatch"' error.
>> Some of my functions fail because they rely on functions that call 
>> annotation(AffyBatch). 
>>
>> My questions are (1) is this the expected behaviour and if yes (2) how am I 
>> and/or upstream maintainers supposed to elegantly deal with it?
> 
> Hi Laurent -- I just came across this issue myself -- package A failed
> because it called a function in package B which had a dependency on
> package C which, due to changes in package D, now attached IRanges to
> the search path. Package B then found IRange::annotation on the search
> path, instead of Biobase::annotation.
> 
> The solution was easy, in the end -- add
> 
>   importMethodsFrom(Biobase, annotation)
> 
> to the NAMESPACE of package B, and move Biobase from 'Depends:' to
> 'Imports:' in package B, which is definitely the Right Thing To Do. It
> doesn't matter now that IRanges is on the user search path, package B
> always gets the function it wants.
> 
> The solution is less elegant for a function that is not in a name
> space, e.g., because the user is writing it in the global environment,
> as in your example below. Then the solution is to use
> 
>   Biobase::annotation(eset)
> 
> in place of annotation(eset).
> 
> There might be additional technical solutions that Biobase / IRanges /
> Biostrings package authors can explore for this particular case...
> 
> Martin
> 
>> Illustrative code and sessionInfo are given below.
>>
>> I hope that I am not missing anything obvious here.
>>
>> Thank you in advance.
>>
>> Laurent
>>
>>
>> -- R code ---------------------------------------
>>> source("http://bioconductor.org/biocLite.R")
>>> update.packages(rep=biocinstallRepos(), ask=FALSE)
>>> library(affydata)
>> Loading required package: affy
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>>   Vignettes contain introductory material. To view, type
>>   'openVignette()'. To cite Bioconductor, see
>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>>> data(Dilution)
>>> annotation(Dilution)
>> [1] "hgu95av2"
>>> library(IRanges)
>> Attaching package: 'IRanges'
>>
>>
>> 	The following object(s) are masked from package:Biobase :
>>
>> 	 annotation,
>> 	 annotation<- 
>>
>>
>> 	The following object(s) are masked from package:base :
>>
>> 	 cbind,
>> 	 order,
>> 	 pmax,
>> 	 pmax.int,
>> 	 pmin,
>> 	 pmin.int,
>> 	 rbind,
>> 	 rep.int,
>> 	 table 
>>
>>> annotation(Dilution)
>> Error in function (classes, fdef, mtable)  : 
>>   unable to find an inherited method for function "annotation", for signature 
>> "AffyBatch"
>>> Biobase:::annotation(Dilution)
>> [1] "hgu95av2"
>>> sessionInfo()
>> R version 2.9.0 Under development (unstable) (2009-02-12 r47911) 
>> i686-pc-linux-gnu 
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>>
>> other attached packages:
>> [1] IRanges_1.1.38  affydata_1.11.3 affy_1.21.7     Biobase_2.3.10 
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.11.3        preprocessCore_1.5.3 tools_2.9.0
>>
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>