[BioC] gene2pathway: Error in pathIDsLev1

[Dick Beyer]

Hi,

I get the "Error in pathIDsLev1" error when using the gene2pathway retrain() function.

> retrain(minnmap=30, level1Only="Metabolism", level2Only="Genetic Information Processing", organism="hsa", gene2Domains=NULL, KEGG.package=TRUE, remove.duplicates=FALSE, use.bagging=TRUE, nbag=11)
Retrieving KEGG information via KEGG.db package ...
Error in pathIDsLev1[sapply(level1Only, function(l) grep(l, names(pathIDsLev1)))] :
   invalid subscript type 'list'
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-redhat-linux-gnu

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
  [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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] org.Hs.eg.db_2.3.6  RCurl_1.3-0         bitops_1.0-4.1      gene2pathway_1.4.0  org.Dm.eg.db_2.3.5  RBGL_1.22.0         graph_1.24.1
  [8] KEGGSOAP_1.20.0     biomaRt_2.2.0       KEGG.db_2.3.5       RSQLite_0.7-3       DBI_0.2-4           AnnotationDbi_1.8.1 Biobase_2.6.0
[15] kernlab_0.9-9

loaded via a namespace (and not attached):
[1] SSOAP_0.5-4     tools_2.10.0    XML_2.6-0       XMLSchema_0.1-4

Would anyone have a suggestion as what to do next?

Thanks very much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer