[BioC] error in ls() unused arguments

[Patrick Wijchers]

I guess my saved session is problematic...
To confirm this, I started a new folder and made new objects and there, 
everything works like a charm.

However, I can still access all my objects, so it appears all my work 
and data is not lost.... thank god for that as a start to the weekend!

Is there a easy way to access these objects in a different folder, e.g. 
by copying or editing them into a new R session? Or does this mean I 
will have to spend some time to reproduce all my data in new session 
(which should be a lot quicker second time around)?

Again, thank you very much for your help,

Patrick

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

-- 
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