Dear developers, has anyone experienced the problem described below? Is it a bug in handling interrupts in R?
Best, Oleg -------- Original Message -------- Subject: Re: [BioC] 'recursive default argument' error in GOENTREZID2GO From: Diego Diez <[EMAIL PROTECTED]> ...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" <[EMAIL PROTECTED]> 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 > > _______________________________________________ > Bioconductor mailing list > [EMAIL PROTECTED] > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
