[BioC] gene2pathway: Error in pathIDsLev1

[Jean-Pierre DESVIGNES]

Dick Beyer <dbeyer <at> u.washington.edu> writes:

> 
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at ...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 

Hello Dick,

I have the same error.
I check the code and in the function "gene2pathway:::getKEGGHierarchy"
there are :  
kegg = RCurl:::getURL("ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg")
kegg = unlist(strsplit(kegg, "\n"))
level1 = grep("A<B>", kegg)
level2 = grep("B  <b>", kegg)
level3 = grep("PATH", kegg)
...

But if you look at the URL, in the file we found :

"A<b>01100 Metabolism</b>"
"B"
"B  <b>01101 Carbohydrate Metabolism</b>"
...


I don't know if this error has been corrected or if it will be in a futur
version (with Bioc 2.6)


Jean-Pierre