Q:Gage R package: kegg.gsets function

[algirdas]

Hi all,

I can not download latest kegg definitions using gage package (kegg.sets function). I tried on different computers. Error messages:

> kg.human <- kegg.gsets("human")
Error in names(kg.sets) = paste(species, ks.names, sep = "") :
'names' attribute [1] must be the same length as the vector [0]

> kg.hsa=kegg.gsets("hsa")
Error in names(kg.sets) = paste(species, ks.names, sep = "") :
'names' attribute [1] must be the same length as the vector [0]

> kg.mouse<- kegg.gsets("mouse")
Error in FUN(X[[i]], ...) : subscript out of bounds

How to fix this problem?
Thanks,
AK

[Dameon]

I get the same error. The paths/urls must have changed on the Kegg repository backend. It looks like the error might be coming from the keggLink function call from within kegg.gsets.

[bigmw]

This problem indeed came from KEGG REST API. They have fixed it, and kegg.gsets() in gage package works now. For more details:

https://support.bioconductor.org/p/72417/

[Dameon]

Awesome. Thank you for looking into this for us.