"EXTID2PATHID" error in DOSE

[carlossainz813]

I've been having an issue with the DOSE package, specifically with the functions that call on Disease Ontology (enrichDO, and gseDO).
This is the code that I have been using.

          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),  
                        readable      = FALSE)

However, whenever I run the code I get this error:
Error in get("EXTID2PATHID", envir = USER_DATA) :
object 'EXTID2PATHID' not found

I am unsure what is happening, as it used to work before, but now it gives me this error directly. I've tried uninstalling and reinstalling DOSE and all its dependencies but haven't managed to solve the issue.

[GuangchuangYu]

I pasted your code into R and it works fine.

Please make sure you are using the latest release version.

[LXT3600]

I'm having the same issue. Have you solved it?

[carlossainz813]

It seemed that there was an issue when I updated R from R4.4.1 into R4.4.2. I deleted R4.4.2 and reinstalled R4.4.1 and installed clusterprofiler and DOSE again and it seemed to work fine. I would suggest you try the same.

[LXT3600]

Thank you so much

…

---Original--- From: "Carlos ***@***.***> Date: Mon, Jan 13, 2025 22:37 PM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [YuLab-SMU/DOSE] "EXTID2PATHID" error in DOSE (Issue #86) It seemed that there was an issue when I updated R from R4.4.1 into R4.4.2. I deleted R4.4.2 and reinstalled R4.4.1 and installed clusterprofiler and DOSE again and it seemed to work fine. I would suggest you try the same. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[LXT3600]

thank you so much

…

---Original--- From: "Carlos ***@***.***> Date: Mon, Jan 13, 2025 22:37 PM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [YuLab-SMU/DOSE] "EXTID2PATHID" error in DOSE (Issue #86) It seemed that there was an issue when I updated R from R4.4.1 into R4.4.2. I deleted R4.4.2 and reinstalled R4.4.1 and installed clusterprofiler and DOSE again and it seemed to work fine. I would suggest you try the same. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[elanur-yilmaz]

I am also having the same issue. I ran it last week (January 23rd) with the R version 4.4.2 but now I am getting the same error:

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

I uninstalled re-installed many times but nothing worked.
Is there any other way to fix it without changing the R version? Any suggestion?

[elanur-yilmaz]

here is the update, if I ran enrichDO with the clusterProfiler library, it works. However, if I use library(DOSE), it gives the error. So for enrichDO, I would suggest to run with library(clusterProfiler) only.

[Tetraenali]

Can't repeat any results of enrichDO from several files generate from last year. It always come to weird issues using DOSE. Don't know why can't map to any term.

[andysw90]

I think core issue is a call to GOSemSim:::get_onto_data here which throws a C exception when ontology is "HDO"

[guidohooiveld]

FWIW: the code in the first post also works in my hands.

Also: if you would like to limit the background to some list of genes, you will need to set the option: options(enrichment_force_universe = TRUE). The default value = FALSE).

See: YuLab-SMU/clusterProfiler#283 (comment)

> library(DOSE)  
> library(org.Hs.eg.db)  
> library(clusterProfiler)  
>       
> data(geneList)  
>
> gene <- names(geneList)[abs(geneList) > 1.5]  
> head(gene)  
[1] "4312"  "8318"  "10874" "55143" "55388" "991"  
> 
> 
> ## to limit universe to 'background'
> options(enrichment_force_universe = TRUE) 
> 
> universe <- unique( names(geneList) )
> 
> x <- enrichDO(gene          = gene,  
+               ont           = "HDO",  
+               organism      = "hsa",  
+               pvalueCutoff  = 0.05,  
+               pAdjustMethod = "BH",  
+               universe      = universe,  
+               readable      = FALSE)
> 
> x
#
# over-representation test
#
#...@organism    Homo sapiens 
#...@ontology    HDO 
#...@keytype     ENTREZID 
#...@gene        chr [1:513] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" ...
#...pvalues adjusted by 'BH' with cutoff <0.05 
#...374 enriched terms found
'data.frame':   374 obs. of  12 variables:
 $ ID            : chr  "DOID:1612" "DOID:5093" "DOID:193" "DOID:10534" ...
 $ Description   : chr  "breast cancer" "thoracic cancer" "reproductive organ cancer" "stomach cancer" ...
 $ GeneRatio     : chr  "35/273" "35/273" "39/273" "25/273" ...
 $ BgRatio       : chr  "398/12495" "398/12495" "493/12495" "205/12495" ...
 $ RichFactor    : num  0.0879 0.0879 0.0791 0.122 0.0823 ...
 $ FoldEnrichment: num  4.02 4.02 3.62 5.58 3.77 ...
 $ zScore        : num  9.17 9.17 8.87 9.89 8.28 ...
 $ pvalue        : num  1.72e-12 1.72e-12 2.32e-12 2.69e-12 9.57e-11 ...
 $ p.adjust      : num  5.19e-10 5.19e-10 5.19e-10 5.19e-10 1.30e-08 ...
 $ qvalue        : num  2.31e-10 2.31e-10 2.31e-10 2.31e-10 5.78e-09 ...
 $ geneID        : chr  "4312/6241/983/2146/3887/6790/891/23532/3161/993/5347/55215/55723/875/8438/9700/5888/7083/898/1493/6352/4288/355"| __truncated__ "4312/6241/983/2146/3887/6790/891/23532/3161/993/5347/55215/55723/875/8438/9700/5888/7083/898/1493/6352/4288/355"| __truncated__ "4312/7153/259266/6241/983/10232/332/2146/9212/8208/6790/891/23532/993/8061/5347/4318/10615/6890/875/3159/5888/7"| __truncated__ "4312/2305/10403/259266/8140/81930/332/2146/8061/4318/3576/8792/6352/4288/3131/2952/347902/3572/563/7031/6926/31"| __truncated__ ...
 $ Count         : int  35 35 39 25 32 34 36 34 18 31 ...
#...Citation
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics. 2015, 31(4):608-609 

> 
> packageVersion("DOSE")
[1] ‘4.0.0’
> packageVersion("clusterProfiler")
[1] ‘4.14.6’
> 
> R.Version()$version.string
[1] "R version 4.4.2 (2024-10-31 ucrt)"
> 
> 

[sd68515]

Same here.

[guidohooiveld]

@sd68515 : what exactly do you mean?

If your code is not working, could you please check using the example data + code I posted above, and report back?

Also, post as much info as possible on your problem, including your code and input data. Only this will allow others to give feedback.

This thread may also be of interest: YuLab-SMU/clusterProfiler#765

[sd68515]

@guidohooiveld : Hey, please be patient and don't take this the wrong way! I'm having the exact same issue as OP - your 'helpful info' didn't actually help at all. This problem might be related to the user's internet connection though. If the database 'reference files' don't download completely, this error pops up.

[DarioS]

I have a reproducible example. To begin with, Install only DOSE in a fresh R library.

install.packages("BiocManager")
BiocManager::install("DOSE")

Then, run an analysis.

library(DOSE)
data(geneList)
gseDO(geneList)
  Error in loadNamespace(x) : there is no package called ‘rappdirs’

There is an error about a missing undeclared dependecy. So, I install it by install.packages("rappdirs").

> gseDO(geneList)
  preparing geneSet collections...
  Error in get("PATHID2EXTID", envir = USER_DATA) : 
    object 'PATHID2EXTID' not found

So, I can trigger the error about the missing database. I used the latest version or R.

> sessionInfo() # Today's R development daily build.
  R Under development (unstable) (2025-07-07 r88391 ucrt)
  Platform: x86_64-w64-mingw32/x64
  Running under: Windows 10 x64 (build 19045)

  other attached packages:
    DOSE_4.3.0

But if I close R, reopen it, and use the same test code of analysis, it works!

> library(DOSE)
  DOSE v4.3.0 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
> data(geneList)
> gseDO(geneList)
  preparing geneSet collections...
  GSEA analysis...
  leading edge analysis...
  done...

  # Gene Set Enrichment Analysis
  #
  #...@organism    Homo sapiens 
  #...@setType     HDO 
  #...@keytype     ENTREZID 
  #...@geneList    Named num [1:12495] 4.57 4.51 4.42 4.14 3.88 ...
   - attr(*, "names")= chr [1:12495] "4312" "8318" "10874" "55143" ...
  #...nPerm        
  #...pvalues adjusted by 'BH' with cutoff <0.05 
  #...59 enriched terms found

I find that DOSE package does not use on.exit to make changes when R closes, so I can't explain it.

[ray1919]

{
        tryCatch(utils::data(list="DGN_EXTID2PATHID", package="DOSE"))
        tryCatch(utils::data(list="DGN_PATHID2EXTID", package="DOSE"))
        tryCatch(utils::data(list="DGN_PATHID2NAME", package="DOSE"))
        EXTID2PATHID <- DGN_EXTID2PATHID <- get("DGN_EXTID2PATHID")
        PATHID2EXTID <- DGN_PATHID2EXTID <- get("DGN_PATHID2EXTID")
        PATHID2NAME <- DGN_PATHID2NAME <- get("DGN_PATHID2NAME")
        
        rm(DGN_EXTID2PATHID, envir = .GlobalEnv)
        rm(DGN_PATHID2EXTID, envir = .GlobalEnv)
        rm(DGN_PATHID2NAME, envir = .GlobalEnv)
}

code from enrichDGN works