[BioC] problems with GO package data

[Yu-An Dong]

Hi Robert,
I started R in a clean directory and loaded GO:

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

However, R simply hanged there and I had to use ^-C to interrupt. But 
when I issued the command
a second time, I immediately got the same error as before:

 > GOLOCUSID2GO[["4121"]]
Fehler: rekursive Standardargument Referenz ("Error: recursive standard 
argument reference")
 > traceback()
Kein traceback vefügbar ("No traceback available")

 > sessionInfo()
R version 2.2.0, 2005-10-06, i686-pc-linux-gnu

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

other attached packages:
      GO
"1.10.0"

Mm, strange... Again, I appreciate your help!
Best wishes,
Yu-An







Robert Gentleman wrote:
> 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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