[BioC] problems with GO package data

Yu-An Dong yu-an.dong at bio.ifi.lmu.de
Thu Feb 2 16:00:42 CET 2006 

Yes, this time it worked! Seems ^-C caused the problem - since I was 
first time using GO from BioC/R, I didn't expect it to take
that long and wasn't patient enough. Again, thanks for all your help!
Best,
Yu-An


Robert Gentleman wrote:
> Jim makes a good point here. With the system we are currently using, 
> all of the data are stored in files and loaded on demand. That means 
> that the first query is always going to be slow (and possibly really 
> slow on some systems with limited RAM), subsequent queries will be 
> fast. We are working on a new system that will speed things up 
> substantially.
>
> Hitting control-C could certainly do odd things (but I would have 
> expected general odd things), like no calls to [[ to work, not just 
> this particular one - now maybe that is the case (and if so, could you 
> let us know Yu-An?)
>
>  best wishes
>   Robert
>
>
> James W. MacDonald wrote:
>> 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
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>

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