[BioC] problems with GO package data
Robert Gentleman
rgentlem at fhcrc.org
Tue Jan 31 17:46:12 CET 2006
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
>>>>>
>>>>
>>>
>>
>
>
--
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
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