SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Q:Gage R package: kegg.gsets function (http://seqanswers.com/forums/showthread.php?t=62897)

algirdas 09-22-2015 04:47 AM

Q:Gage R package: kegg.gsets function
 
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 09-22-2015 11:58 AM

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 10-02-2015 06:06 PM

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 10-02-2015 06:08 PM

Awesome. Thank you for looking into this for us.


All times are GMT -8. The time now is 09:43 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.