[BioC] 'recursive default argument' error in GOENTREZID2GO
James W. MacDonald
jmacdon at med.umich.edu
Mon Jun 11 17:34:22 CEST 2007
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
> James W. MacDonald wrote:
>> Hi Oleg,
>> Oleg Sklyar wrote:
>>> 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.
>>> > sessionInfo()
>>> R version 2.5.0 (2007-04-23)
>>> attached base packages:
>>>  "splines" "tools" "stats" "graphics" "grDevices" "utils"
>>>  "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"
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
More information about the Bioconductor