[BioC] annaffy errors

[James W. MacDonald]

Hi Ido,

One problem is that your GO and KEGG packages are absolutely ancient. 
The current versions are 1.14.1, so you need to update those.

I use annaffy all the time, and I don't see these errors, so try 
updating GO and KEGG and see if that fixes things.

Best,

Jim



Ido M. Tamir wrote:
> Hi,
> 
> I am getting errors from annaffy when I try to use it
> on "mgu74av2", depending on what columns I request/exclude
> or call the function a second time:
> 
> 
>>  anncols <- aaf.handler() #all!
>>  andiff <- aafTableAnn(probeTop, "mgu74av2", anncols )
> 
> Error in `parent.env<-`(`*tmp*`, value = NULL) : 
> 	use of NULL environment is defunct
> 
>> andiff <- aafTableAnn(probeTop, "mgu74av2", anncols )
> 
> Error in exists(num$GOID, GOTERM) : recursive default argument reference
> 
> In an old post I found this could be because of conflicting package versions.
> I reinstalled  mgu74av2 and annaffy but this did not help.
> 
> Thank you very much in advance,
> ido
> 
> 
> 
>>sessionInfo()
> 
> R version 2.4.1 (2006-12-18) 
> x86_64-redhat-linux-gnu 
> 
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    
> [7] "datasets"  "methods"   "base"     
> 
> other attached packages:
>       annaffy          KEGG            GO      mgu74av2 mgu74av2probe 
>       "1.6.1"      "1.10.0"      "1.10.0"      "1.14.0"      "1.14.0" 
>   mgu74av2cdf         limma  affyQCReport    simpleaffy    genefilter 
>      "1.14.0"       "2.9.1"      "1.12.0"       "2.8.0"      "1.12.0" 
>      survival         plier         gcrma   matchprobes   geneplotter 
>        "2.30"       "1.4.0"       "2.6.0"       "1.6.0"      "1.12.0" 
>      annotate          affy        affyio       Biobase 
>      "1.12.1"      "1.12.2"       "1.0.0"      "1.12.2"
> 
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-- 
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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