[BioC] error in ls() unused arguments

[Patrick Wijchers]

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    */

-- 
Patrick Wijchers, PhD
MRC Clinical Sciences Centre
Imperial College London
Hammersmith Campus
Du Cane Road
London W12 0NN
Phone:	+44 (0)20 8383 8500 (office)
	+44 (0)20 8383 8317 (lab)
Fax:	+44 (0)20 8383 8306
Email: 	patrick.wijchers at csc.mrc.ac.uk