[BioC] problems with GO package data

[Ting-Yuan Liu]

Hi Yu-An,

I still cannot reproduce the same error even I switch to an 
i686-pc-linux-gnu machine.  Here are some suggestions:

(1) re-install GO package
(2) not using the natural language support.  Use English for your R and 
try again.

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Sat, 28 Jan 2006, Yu-An Dong wrote:

> Hi Ting-Yuan,
> 
> I still get the same problem, e.g.
> 
> > GOLOCUSID2GO[["4121"]]
> Fehler: rekursive Standardargument Referenz
> 
> The error message says: "Error: recursive standard argument reference". Here's
> my
> session info:
> 
> > sessionInfo()
> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
> hgu95av2    GOstats   multtest genefilter   survival     xtable       RBGL
> "1.10.0"    "1.4.0"    "1.8.0"    "1.8.0"     "2.20"    "1.3-0"    "1.6.0"
> annotate    Biobase         GO      graph      Ruuid    cluster
> "1.8.0"    "1.8.0"   "1.10.0"    "1.8.0"    "1.8.0"   "1.10.2"
> 
> Any suggestions? Thanks!
> 
> Yu-An
> 
> 
> 
> Ting-Yuan Liu wrote:
> > Hi Yu-An,
> > 
> > I think the error message is not written in English, right?  Could you
> > translate it to English so that it will be more helpful.
> > 
> > I cannot reproduce the same error in my machine, and here is the result:
> > 
> > > GOLOCUSID2GO[["4121"]]
> > > 
> > $"GO:0005975"
> > $"GO:0005975"$GOID
> >         IEA
> > "GO:0005975"
> > 
> > $"GO:0005975"$Evidence
> > [1] "IEA"
> > 
> > $"GO:0005975"$Ontology
> > [1] "BP"
> > 
> > 
> > $"GO:0006487"
> > $"GO:0006487"$GOID
> >         IEA
> > "GO:0006487"
> > 
> > $"GO:0006487"$Evidence
> > [1] "IEA"
> > 
> > $"GO:0006487"$Ontology
> > [1] "BP"
> > 
> > .... skip ...
> > 
> > Here is the result of my sessionInfo():
> > 
> > > sessionInfo()
> > > 
> > R version 2.2.1, 2006-01-04, x86_64-unknown-linux-gnu
> > 
> > attached base packages:
> > [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> > "datasets"
> > [7] "base"
> > 
> > other attached packages:
> >      GO
> > "1.10.0"
> > 
> > 
> > Could you also provide the sessionInfo() output for more information
> > please?  Thanks.
> > 
> > Ting-Yuan
> > ______________________________________
> > Ting-Yuan Liu
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > Seattle, WA, USA
> > ______________________________________
> > 
> > On Wed, 25 Jan 2006, Yu-An Dong wrote:
> > 
> > 
> > > Hello, I've installed BioC 1.7 (with R 2.2.0) without problem. The GO
> > > package was installed but I can't
> > > access the data:
> > > 
> > > > GOLOCUSID2GO[["4121"]]
> > > Fehler: rekursive Standardargument Referenz
> > > 
> > > And I get similar error messages with the other functions in the GO
> > > package. Any suggestions? Thanks!
> > > 
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > 
> > > 
> 
> 
>