[BioC] 'recursive default argument' error in GOENTREZID2GO

[Wolfgang Huber]

Hi Oleg,

1. as Seth pointed out, if there is a patched versions of the latest 
release of R (as there is now), then it would be helpful to test and 
report bugs on that, rather than on the release. There is not so much 
point in spending time on problems that may already have been fixed. See
http://cran.at.r-project.org/sources.html

2. AfaIu, it is not safe to assure that R behaves well after an 
interrupt (Ctrl-C). It may well do so in most cases, and it probably 
does for Ctrl-C encountered during running most of the code in R itself, 
but I would be surprised if all contributed packages allowed Ctrl-C only 
then when it is safe. (I would be happy to be proven wrong.)

  Best wishes
   Wolfgang



> Does not it look like a bug in R, Should not it be reported as such, 
> Diego could you maybe do that? I did hit many ^C before getting my error 
> as I had large objects and often used ^C to terminate printing. And 
> well, quitting R is *not* a solution, such things run in scripts and 
> need to be stable.
> 
> Best,
> Oleg
> 
> Diego Diez wrote:
>> Hi Oleg, James and Seth.
>>
>> I also found the same problem (or very close) and used the same approach 
>> mentioned by James to solve it, which works fine but still it too 
>> annoying. After reading the post I've tried to reproduce the steps that 
>> use to reach me to that point. It happens with any environment, or at 
>> least annotation packages stored as environments. I can't think of any 
>> reason why this happens but let me show you the code:
>>
>>  > library(rae230a)
>>  > xx <- as.list(rae230aENTREZID)
>> ^C
>>  > xx <- as.list(rae230aENTREZID)
>> Error in as.list(rae230aENTREZID) : recursive default argument reference
>>
>> now, while the as.list() is working, cancel the process with control-C, 
>> and after that, the mentioned error happens whenever you try to repeat 
>> the process of transforming the environment to a list. The cancel must 
>> be done soon after hitting return, I found one case when delaying a 
>> little made me unable to reproduce the error. Other environments found 
>> in the package are not affected (i.e. rae230aSYMBOL, rae230aGENENAME, etc).
>>
>> Going deeper to the problem, I found that canceling the environment 
>> "loading" with any function reproduces the problem:
>>
>>  > is(rae230aSYMBOL)
>> ^C
>>  > is(rae230aSYMBOL)
>> Error in .class1(object) : recursive default argument reference
>>  > rae230aSYMBOL
>> Error: recursive default argument reference
>>
>> By "loading" a mean that the first time I execute as.list(rae230aSYMBOL) 
>> or is(rae230aSYMBOL) there is a delay which I assume is the environment 
>> being loaded into memory. Any further execution of the same commands 
>> will occur almost immediately.
>>
>> So, why should I cancel an environment loading soon after trying to load 
>> it? It happens that I was loading an environment inside a function, ran 
>> the function and wanted to cancel the execution, thus, the error 
>> appeared and the environemnt was unusable. Anyway, this seems to me more 
>> an R related issue.
>>
>> HTH,
>>
>> Diego.
>>
>>
>>  > sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> powerpc-apple-darwin8.9.1
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
>> [7] "base"
>>
>> other attached packages:
>>  rae230a
>> "1.16.0"
>>  >
>>
>>
>>
>> On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote:
>>
>>> "James W. MacDonald" <jmacdon at med.umich.edu> writes:
>>>
>>>> Hi Oleg,
>>>>
>>>> Oleg Sklyar wrote:
>>>>> Hi,
>>>>>
>>>>> anybody has an idea as for the following error, the example is actually
>>>>> from the GO package examples. Thanks, Oleg
>>>>>
>>>>>> library(GO)
>>>>>> egId <- "10043"
>>>>>> egIdGoData <- GOENTREZID2GO[[egId]]
>>>>> Error: recursive default argument reference
>>>> I sometimes see that error as well. I have no idea what causes it, as it
>>>> doesn't seem repeatable. Anyway, quitting R and starting over has always
>>>> fixed the problem for me.
>>> Oleg, is this reproducible for you?  I wasn't able to get the error.
>>> Have you tried updating to R patched?
>>>
>>> + seth
>>>
>>> --Seth Falcon | Computational Biology | Fred Hutchinson Cancer 
>>> Research Center
>>> http://bioconductor.org
>>>
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> 


-- 

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber