"EXTID2PATHID" error in DOSE

Question

[nizamov.1999]

Hi!

I have an issue with DOSE package for the last week.

When I'm trying to run this code:

library(DOSE)  
library(org.Hs.eg.db)  
library(clusterProfiler)  

data(geneList)  

gene <- names(geneList)[abs(geneList) > 1.5]  
head(gene)  

x <- enrichDO(gene          = gene,  
              ont           = "HDO",  
              organism = "hsa",  
              pvalueCutoff  = 0.05,  
              pAdjustMethod = "BH",  
              universe      = names(geneList),  
              minGSSize     = 5,  
              maxGSSize     = 500,  
              qvalueCutoff  = 0.05,  
              readable      = FALSE)

It returns with:

Error in get("EXTID2PATHID", envir = USER_DATA) :
object 'EXTID2PATHID' not found

I don't know how but it worked without any issue earlier. I encounter this error both in Windows version and in Linux version for servers.
Maybe someone knows a solution to this issue?

[andysw90]

Did you manage to resolve this? I'm having the same issue. It works for other ontologies, but I want to use HDO!