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

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?

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.