[Bioc-devel] Biobase/IRanges annotation maksing
l.gatto at dnavision.be
Wed Feb 18 12:41:55 CET 2009
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
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.
-- R code ---------------------------------------
> update.packages(rep=biocinstallRepos(), ask=FALSE)
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)'.
Attaching package: 'IRanges'
The following object(s) are masked from package:Biobase :
The following object(s) are masked from package:base :
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "annotation", for signature
R version 2.9.0 Under development (unstable) (2009-02-12 r47911)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 IRanges_1.1.38 affydata_1.11.3 affy_1.21.7 Biobase_2.3.10
loaded via a namespace (and not attached):
 affyio_1.11.3 preprocessCore_1.5.3 tools_2.9.0
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