[BioC] Error in .nextMethod(e1, e2) with updated R and bioC package on MAC OS

[Anat Caspi]

Hi Martin,

Thanks for your response. 
I've repeated the package installation as you recommended, in a new run of R.
I checked that I do not have any bioC packages loaded by default:
] getOption("defaultPackages")
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"

I also checked to see that I'm running v. 2.6.2:

the following was the message at startup-
R version 2.6.2 (2008-02-08)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

and I also invoked sessionInfo()
] sessionInfo()
R version 2.6.2 (2008-02-08)
powerpc-apple-darwin8.10.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.2

I then followed by:
]    source("http://bioconductor.org/biocLite.R")
]    update.packages(repos=biocinstallRepos(), ask=FALSE)
The output began with:
"
also installing the dependency 'limma'

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/limma_2.12.0.tgz\
'
Content type 'application/x-gzip' length 1064773 bytes (1.0 Mb)
opened URL
..."

All subsequent packages passed with no warnings or errors except:

"
Error: cannot remove prior installation of package 'limma'
"

which is strange because it had just installed 'limma' as the first dependency.

Not sure where to go from here.
Thanks so much for your response.
Anat.