[BioC] 'recursive default argument' error in GOENTREZID2GO

Diego Diez diez at kuicr.kyoto-u.ac.jp
Tue Jun 12 04:42:04 CEST 2007

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  

 > library(rae230a)
 > xx <- as.list(rae230aENTREZID)
 > 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)
 > 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.



 > sessionInfo()
R version 2.5.0 (2007-04-23)


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

other attached packages:

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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