[BioC] error in ls() unused arguments

[Patrick Wijchers]

Thanks for your quick response. If I use R --vanilla I can load the 
affyPLM package without problems:
/*> library(affyPLM)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
Loading required package: preprocessCore*/

However, now, my objects seem to be gone:
/*> ls()
character(0)
 > objects()
character(0)*/

Any idea why?

Thanks again,

Patrick

Laurent Gautier wrote:
>
>
> 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    */
>>
>

-- 
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