[Bioc-devel] Biobase/IRanges annotation maksing

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