[BioC] error in ls() unused arguments

[Laurent Gautier]

Is this this happening when starting R like:

R --vanilla

?

Patrick Wijchers wrote:
> Dear all,
> 
> I encountered a problem while working on R that I do not know how to solve.
> It started when I wanted to load the affyPLM package:
> */> library(affyPLM)
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: splines
> Loading required package: preprocessCore
> Error in ls(where) : unused argument(s) (2)
> Error in library(affyPLM) : .First.lib failed for 'affyPLM'/*
> 
> As packages such as 'affy', 'genefilter' and 'limma' load fine, I 
> thought it might be something related to the affyPLM package.
> However, upon trying to re-install the package, I got a similar error:
> /*> source("http://bioconductor.org/biocLite.R")
> Error in ls(all.names = TRUE) : unused argument(s) (all.names = TRUE)*/
> 
> Now, I think it may be related to the 'ls' function. Strangely enough, 
> when using the 'ls' command I get this:
> /*> ls()
> Quality control information for mouse4302:
> This package has the following mappings:
> Error in get(mapname) : variable "mouse4302ACCNUM" was not found*/
> 
> I can now only access my objects using 'objects()'.
> Strangely, I have been using  all week without problems. I have tried 
> restarting R, even reinstalling R, but to no avail. I hope it is 
> something stupid I do not see.... Does anyone have a suggestion how I 
> can solve this?
> 
> Any help would be greatly appreciated,
> 
> Patrick
> 
> /*> sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-redhat-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] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base   
> other attached packages:
> [1] preprocessCore_1.4.0 gcrma_2.14.1         matchprobes_1.14.1 [4] 
> affy_1.20.0          Biobase_2.2.1        RSQLite_0.7-1      [7] 
> DBI_0.2-4         
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1       annotate_1.20.1     AnnotationDbi_1.4.2
> [4] genefilter_1.22.0   mouse4302.db_2.2.5  survival_2.34-1    */
>