[BioC] GOALLLOCUSID error [GOstats]

[James W. MacDonald]

Hi Wenjian,

Wenjian Yang wrote:
> Hi, I'm using R 2.3.1 and GOstats_1.6.0
>
> When I tried GOALLLOCUSID$"GO:0000158", I got the error message
> "Error: recursive default argument reference"
>
> GOLOCUSID worked fine.
>
> In addition, during the installation of GOstats via biocLite, the "RBGL"
> packages failed to compile, but I don't think that should affect the problem
> with GOALLLOCUSID.
>
> Did anybody encouter the problem as well?
>   
Sometimes I see this same error, and I don't have a good fix because I 
don't know why I see it. However, it appears to me that a simple restart 
of R fixes things.

BTW, this works for me with the version of GO I have.

 > library(GO)
 > GOALLLOCUSID$"GO:0000158"
     TAS      IDA      TAS      TAS      IDA      TAS      RCA      TAS
"851217" "851339" "851339" "851421" "851647" "852685" "853065" "854179"
     ISS      ISS      IMP      ISS      NAS      ISS      TAS       NR
"855766"  "39337"  "45959"  "45959"  "45959"  "47877"   "5516"   "5519"
     IDA      ISS      RCA      TAS      IEA      RCA      RCA      RCA
  "5520"  "28227"  "19052"  "19052"  "19053"  "19053"  "19055"  "63953"
     RCA      RCA      IEA      TAS      IDA      IEA      IEA      IEA
 "67857"  "71978"  "24672"  "24672"  "24673"  "24673"  "24674"  "63995"
     IEA      ISS      IEA      IEA
"117104" "117281" "171121" "315648"
 > sessionInfo()
Version 2.3.1 (2006-06-01)
i386-pc-mingw32

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"    

other attached packages:
      GO
"1.12.0"

Best,

Jim

> Thanks.
>
> Wenjain Yang
>
> 	[[alternative HTML version deleted]]
>
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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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