[BioC] problems with GO package data

[James W. MacDonald]

Yu-An,

Could the problem be impatience on your part? On both WinXP and Linux 
this takes a bit of time for me (using either R-2.2.0 or R-2.3.0):

 > library(GO)
 > system.time(GOLOCUSID2GO[["4121"]])
[1] 30.94  0.57 31.53    NA    NA

Note that any further queries of this sort take no time at all:

 > system.time(GOLOCUSID2GO[["4121"]])
[1]  0  0  0 NA NA
 > system.time(GOLOCUSID2GO[["4122"]])
[1]  0  0  0 NA NA


Best,

Jim

Robert Gentleman wrote:
> OK, well the next option is to move to the current version of R
> (which is not 2.2.0) and see if your problems persist. I cannot 
> replicate the bug on any system I have access to. And since [[ takes one 
> argument, it is hard to see how it has  a recursive standard 
> argument...someone is confused (maybe overoptimized compiling, but even 
> that is very rare these days).
> 
> Or you to get more serious about debugging. Which will most likely 
> involve getting gdb or some similar interface to it working so you can 
> probe the internals.
> 
> sorry
>    Robert
> 
> Yu-An Dong wrote:
> 
>>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
>>>>>>
>>>>>>
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioconductor mailing list
>>>>Bioconductor at stat.math.ethz.ch
>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>
>>>
>>
> 


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623