[Rd] bug in R environments? Was: [BioC] 'recursive default argument' error...

From: Oleg Sklyar <osklyar_at_ebi.ac.uk>
Date: Tue, 12 Jun 2007 09:24:12 +0100

Dear developers,

has anyone experienced the problem described below? Is it a bug in handling interrupts in R?


...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)

> xx <- as.list(rae230aENTREZID)

Error in as.list(rae230aENTREZID) : recursive default argument reference

now, while the as.list() is working, cancel the process with controlC,  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.

HTH, Diego.

> sessionInfo()

R version 2.5.0 (2007-04-23)


attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[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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> gmane.science.biology.informatics.conductor

Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466

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