[BioC] problems with GO package data

[Robert Gentleman]

Hi,
start a clean R and make sure it does not load any save workspaces.
[If you see this message: [Previously saved workspace restored]
then you need to move to a different directory to start or move the 
saved workspace so it is not automatically loaded]

then go

library(GO)
GOLOCUSID2GO[["4121"]]

if you get an error report it and the output of traceback(). And if not, 
then it is not GO, it is something else, probably a variable you have 
created (or that someone else has) that is interfering with dispatch in 
some odd way. To find out who/what, start adding the libraries you have 
listed, one at a time until the culprit is found.


best wishes
   Robert


Yu-An Dong wrote:
> Hi Ting-Yuan,
> 
> I still get the same problem, e.g.
> 
>  > GOLOCUSID2GO[["4121"]]
> Fehler: rekursive Standardargument Referenz
> 
> The error message says: "Error: recursive standard argument reference". 
> Here's my
> session info:
> 
>  > sessionInfo()
> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
>   hgu95av2    GOstats   multtest genefilter   survival     xtable       RBGL
>   "1.10.0"    "1.4.0"    "1.8.0"    "1.8.0"     "2.20"    "1.3-0"    "1.6.0"
>   annotate    Biobase         GO      graph      Ruuid    cluster
>    "1.8.0"    "1.8.0"   "1.10.0"    "1.8.0"    "1.8.0"   "1.10.2"
> 
> Any suggestions? Thanks!
> 
> Yu-An
> 
> 
> 
> Ting-Yuan Liu wrote:
> 
>>Hi Yu-An,
>>
>>I think the error message is not written in English, right?  Could you 
>>translate it to English so that it will be more helpful.
>>
>>I cannot reproduce the same error in my machine, and here is the result:
>>  
>>
>>>GOLOCUSID2GO[["4121"]]
>>>    
>>
>>$"GO:0005975"
>>$"GO:0005975"$GOID
>>         IEA
>>"GO:0005975"
>>
>>$"GO:0005975"$Evidence
>>[1] "IEA"
>>
>>$"GO:0005975"$Ontology
>>[1] "BP"
>>
>>
>>$"GO:0006487"
>>$"GO:0006487"$GOID
>>         IEA
>>"GO:0006487"
>>
>>$"GO:0006487"$Evidence
>>[1] "IEA"
>>
>>$"GO:0006487"$Ontology
>>[1] "BP"
>>
>>.... skip ...
>>
>>Here is the result of my sessionInfo():
>>  
>>
>>>sessionInfo()
>>>    
>>
>>R version 2.2.1, 2006-01-04, x86_64-unknown-linux-gnu
>>
>>attached base packages:
>>[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
>>[7] "base"
>>
>>other attached packages:
>>      GO
>>"1.10.0"
>>
>>
>>Could you also provide the sessionInfo() output for more information 
>>please?  Thanks.
>>
>>Ting-Yuan
>>______________________________________
>>Ting-Yuan Liu
>>Program in Computational Biology
>>Division of Public Health Sciences
>>Fred Hutchinson Cancer Research Center
>>Seattle, WA, USA
>>______________________________________
>>
>>On Wed, 25 Jan 2006, Yu-An Dong wrote:
>>
>>  
>>
>>>Hello, I've installed BioC 1.7 (with R 2.2.0) without problem. The GO 
>>>package was installed but I can't
>>>access the data:
>>>
>>> > GOLOCUSID2GO[["4121"]]
>>>Fehler: rekursive Standardargument Referenz
>>>
>>>And I get similar error messages with the other functions in the GO 
>>>package. Any suggestions? Thanks!
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
>>>
> 
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org