[BioC] 'recursive default argument' error in GOENTREZID2GO

[James W. MacDonald]

Oleg Sklyar wrote:
> Well, I had a several GB data set in memory...

Of course you did. I think the probability that you need to restart R is 
in exact inverse to your desire to do so. ;-D

I _have_ tried to detach() the offending package in the past rather than 
doing a clean restart, but of course that doesn't work.

Seth - I have seen this problem intermittently (usually when using 
annaffy, but it's just when trying to pull data out of an env so I don't 
think it is annaffy specific) for years now. I have yet to figure out 
why it happens, mainly because a clean restart of R _always_ clears the 
problem up.

Best,

Jim


> 
> James W. MacDonald wrote:
> 
>> 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.
>>
>> Best,
>>
>> Jim
>>
>>
>>>  > sessionInfo()
>>> R version 2.5.0 (2007-04-23)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C 
>>>
>>>
>>> attached base packages:
>>> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
>>> [7] "datasets"  "methods"   "base"
>>>
>>> other attached packages:
>>>     Category      Matrix     lattice  genefilter    survival    annotate
>>>      "2.2.1" "0.9975-11"    "0.15-4"    "1.14.1"      "2.31"    "1.14.1"
>>>         KEGG       graph     Biobase          GO     biomaRt       RCurl
>>>     "1.16.0"    "1.14.0"    "1.14.0"    "1.16.0"    "1.10.0"     "0.8-0"
>>>          XML
>>>      "1.9-0"
>>>
>>
>>
> 


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


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