[BioC] A bug in either KEGG or KEGGSOAP?

[Sang Chul Choi]

Hi,

I am wondering if this is an old bug eighter in KEGG or KEGGSOAP (v1.28.0).  The version of R is R version 2.14.1 (2011-12-22).

I installed KEGGSOAP, and tried to list pathways.  While list.pathways lists 44, the KEGG website shows 88 pathways.

http://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+gn:T00100
http://www.genome.jp/dbget-bin/www_bget?gn:T00100

Thank you,

SangChul

> source("http://www.bioconductor.org/biocLite.R")
> biocLite("KEGGSOAP")
> library(KEGGSOAP)
> y <- list.pathways("smu")
> length(y)
[1] 44

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] KEGGSOAP_1.28.0        BiocInstaller_1.2.1    goseq_1.6.0           
 [4] BiasedUrn_1.04         geneLenDataBase_0.99.8 RColorBrewer_1.0-5    
 [7] maptools_0.8-14        sp_0.9-93              foreign_0.8-48        
[10] xtable_1.6-0           DESeq_1.6.1            locfit_1.5-6          
[13] lattice_0.20-0         akima_0.5-7            Biobase_2.14.0        
[16] plotrix_3.3-3          GenomicRanges_1.6.4    IRanges_1.12.5