[BioC] error in ls() unused arguments

[Laurent Gautier]

Patrick Wijchers wrote:
> 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?

The problem, as you experience it, seems to be that loading your earlier 
session compromises a number of things.

You could just try saving individual objects of importance into files 
(with the command "save"), and then import them one by one in a fresh R 
session (where attaching library seems to be working).

> 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)?

If you have a file in which all operations are recorded, this should be 
no major issue (beside possibly the computation time).


Hoping this helps,



L.

> 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    */
>>>>>
>>>>
>>>
>>
>