biomaRt - getBM; Error with obtaining a dataset from getBM() function
2
1
Entering edit mode
Zen ▴ 20
@zen-24840
Last seen 3.2 years ago

Hi, I'm trying to create a dataframe that contains the attributes (interpro_description) of each of the correspoding ensemblID found within a column (ensemblID) of another dataframe (joinedData). I've followed the vignette for biomaRt accordingly, but I keep getting the same error. Anyone has any idea how to resolve the error? The code was working prior, but it seems to stop working somehow.

mart <- useMart(biomart= "ENSEMBL_MART_MOUSE")
mart <- useDataset(dataset = 'mmc57bl6nj_gene_ensembl', mart=mart)

getBM(attributes = c("interpro_description"),
              filters= "arrayexpress",
              values= joinedData$ensemblID,
              mart=mart)

Error output: Error in getNodeSet(html, path = "//div[@class='plain-box float-right archive-box']")[[1]] : subscript out of bounds

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] readxl_1.3.1   biomaRt_2.46.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6           cellranger_1.1.0     pillar_1.4.7        
 [4] compiler_4.0.3       BiocManager_1.30.10  dbplyr_2.1.0        
 [7] prettyunits_1.1.1    tools_4.0.3          progress_1.2.2      
[10] bit_4.0.4            tibble_3.0.6         RSQLite_2.2.3       
[13] memoise_2.0.0        BiocFileCache_1.14.0 lifecycle_1.0.0     
[16] pkgconfig_2.0.3      rlang_0.4.10         DBI_1.1.1           
[19] curl_4.3             parallel_4.0.3       fastmap_1.1.0       
[22] dplyr_1.0.4          stringr_1.4.0        httr_1.4.2          
[25] xml2_1.3.2           rappdirs_0.3.3       generics_0.1.0      
[28] S4Vectors_0.28.1     vctrs_0.3.6          askpass_1.1         
[31] IRanges_2.24.1       hms_1.0.0            tidyselect_1.1.0    
[34] stats4_4.0.3         bit64_4.0.5          glue_1.4.2          
[37] Biobase_2.50.0       R6_2.5.0             AnnotationDbi_1.52.0
[40] XML_3.99-0.5         purrr_0.3.4          blob_1.2.1          
[43] magrittr_2.0.1       ellipsis_0.3.1       BiocGenerics_0.36.0 
[46] assertthat_0.2.1     stringi_1.5.3        openssl_1.4.3       
[49] cachem_1.0.3         crayon_1.4.1
biomaRt error getBM • 3.7k views
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1
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 5 hours ago
EMBL Heidelberg

This error comes from an internal call to listEnsemblArchives(). Do you get the same error if you run that function yourself?

That function is really just getting some detail from an Ensembl webpage. If you visit https://www.ensembl.org/info/website/archives/index.html in a browser, does it work? Do you see a list of Ensembl archive sites?

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0
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A call to this function listEnsemblArchives() returns the same error in R.

But I am able to visit this link (https://www.ensembl.org/info/website/archives/index.html) from my browser

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1
Entering edit mode

I haven't done anything between today and yesterday, except restarting R and my computer and the problem seems to be resolved on its own. Haven't had a clue as to why the problem occurred in the first place or what change for it to be resolved.

Regardless, thanks @ Mike Smith for reaching out to assist.

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Entering edit mode

Thanks for reporting back that it's now working. Hopefully it was just temporary issue with the Ensembl site, but thank you for reporting the issue. I'll try to add some better error handling to biomaRt to catch this problem if it occurs again and offer some guidance to users.

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Entering edit mode

Hello, I am confronted with the exact same error and can't seem to get the getBM function to work despite having restarted R. Is there a way to bypass the internal call to listEnsemblArchives()?

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1
Entering edit mode

I am also having the same issue with this error when I run the getBM() function and when I run the function listEnsemblArchives().

When I go to the Website (https://www.ensembl.org/info/website/archives/index.html) I get the following error: "The Ensembl web service you requested is temporarily unavailable. We are working to restore the service as soon as possible, and apologise for any inconvenience caused."

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0
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I am getting this same error right now.

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I am also getting the same error. I just tried now.

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Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 5 hours ago
EMBL Heidelberg

An update for the reports here around 31st May 2021. It looks like the Ensembl site has been restored (currently in Maintenance Mode) which should fix the issue.

I've also patched biomaRt so that if it detects the page containing "The Ensembl web service you requested is temporarily unavailable" (like below) it will try to get information it needs from each of the Ensembl mirror sites in turn. I think this strategy would have prevented the problems of the past few days. The change is currently in the developmental version of biomaRt (2.49.1) and I'll port it to the release branch once I have run a few more tests.

enter image description here

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