[BioC] KEGGSOAP incomplete list.pathways

[kevin [guest]]

hi,

  I'm finding a discrepancy with KEGGSOAP for arabidopsis.  Not all the pathways are returned via list.pathways.  I'm trying to get the text definition of identified pathways

for example:
get.pathways.by.genes('ath:AT5G14780')
[1] "path:ath00630" "path:ath01100"

yet 00630 is not within the 63 pathways:
[1] "path:ath00603"
[1] "path:ath00620"

[1] "path:ath00640"
[1] "path:ath00660"
[1] "path:ath00710"

 I do get a warning:
Warning message:
In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = list(org = org),  :
  data length [125] is not a sub-multiple or multiple of the number of rows [63]

thanks for the help, and let me know if you need more information,
kevin


 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] SSOAP_0.8-0          org.At.tair.db_2.6.4 RSQLite_0.10.0      
[4] DBI_0.2-5            AnnotationDbi_1.16.2 Biobase_2.14.0      
[7] KEGGSOAP_1.28.0     

loaded via a namespace (and not attached):
[1] IRanges_1.12.1  RCurl_1.7-0     XML_3.4-3       XMLSchema_0.1-6


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