[BioC] error in ls() unused arguments

[Laurent Gautier]

Try then

R --no-site-file --no-init-file --no-environ

If you experience trouble again, that means that your saved session is 
problematic. Let's hope not for now.


L.


Patrick Wijchers wrote:
> 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    */
>>>
>>
>