[Bioc-devel] Biobase/IRanges annotation maksing

[Laurent Gatto]

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?

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