Hello,

I am trying to make a OrgDB for S. pombe from NCBI using the following code:

    makeOrgPackageFromNCBI(
    version = "0.1",
    maintainer = "Lan Anh Nguyen <my@mail.jp>",
    author = "Lan Anh Nguyen <my@mail.jp>",
    outputDir = getwd(),
    tax_id = "4896",
    genus = "Schizosaccharomyces",
    species = "pombe",
    rebuildCache = FALSE
    )

However, I got the following error:

Ensembl site unresponsive, trying useast mirror
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt

After calling the traceback(), I got the following message:

15: h(simpleError(msg, call))
14: .handleSimpleError(function (cond) 
    .Internal(C_tryCatchHelper(addr, 1L, cond)), "Unexpected format to the list of available marts.\nPlease check the following URL manually, and try ?listMarts for advice.\nhttps://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt", 
        base::quote(NULL))
13: stop("Unexpected format to the list of available marts.\n", "Please check the following URL manually, ", 
        "and try ?listMarts for advice.\n", request, call. = FALSE)
12: .listMarts(host = host, path = path, port = port, includeHosts = TRUE, 
        httr_config = httr_config, archive = archive, ensemblRedirect = ensemblRedirect, 
        warn = FALSE)
11: .useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose, 
        port = port, ensemblRedirect = ensemblRedirect, httr_config = httr_config)
10: biomaRt::useEnsembl("ensembl", datSet)
9: FUN(X[[i]], ...)
8: lapply(names(datSets), .ensemblMapsToEntrezId, datSets = datSets)
7: lapply(names(datSets), .ensemblMapsToEntrezId, datSets = datSets)
6: unlist(lapply(names(datSets), .ensemblMapsToEntrezId, datSets = datSets))
5: available.ensembl.datasets()
4: tax_id %in% names(available.ensembl.datasets())
3: prepareDataFromNCBI(tax_id, NCBIFilesDir, outputDir, rebuildCache, 
       verbose)
2: NEW_makeOrgPackageFromNCBI(version, maintainer, author, outputDir, 
       tax_id, genus, species, NCBIFilesDir, databaseOnly, rebuildCache = rebuildCache, 
       verbose = verbose)
1: makeOrgPackageFromNCBI(version = "0.1", maintainer = "Lan Anh Nguyen <my@mail.jp>", 
       author = "Lan Anh Nguyen <my@mail.jp>", outputDir = getwd(), 
       tax_id = "4896", genus = "Schizosaccharomyces", species = "pombe", 
       rebuildCache = FALSE)

with this url: https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt

when I read the ?listMarts, it says:

If you browse to the provided URL and find a page that starts with '<MartRegistry>' this is the correct listing and you should report the issue on the Bioconductor support site: https://support.bioconductor.org

Where can I get the help please? Thank you in advance,

Best regards,

Lan Anh

Edit: my sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.52.0              AnnotationForge_1.38.0      AnnotationDbi_1.58.0       
 [4] DESeq2_1.36.0               SummarizedExperiment_1.26.1 Biobase_2.56.0             
 [7] MatrixGenerics_1.8.0        matrixStats_0.62.0          GenomicRanges_1.48.0       
[10] GenomeInfoDb_1.32.2         IRanges_2.30.0              S4Vectors_0.34.0           
[13] BiocGenerics_0.42.0        

loaded via a namespace (and not attached):
 [1] httr_1.4.3               splines_4.2.0            bit64_4.0.5             
 [4] assertthat_0.2.1         BiocFileCache_2.4.0      blob_1.2.3              
 [7] GenomeInfoDbData_1.2.8   Rsamtools_2.12.0         yaml_2.3.5              
[10] progress_1.2.2           pillar_1.7.0             RSQLite_2.2.14          
[13] lattice_0.20-45          glue_1.6.2               digest_0.6.29           
[16] RColorBrewer_1.1-3       XVector_0.36.0           colorspace_2.0-3        
[19] Matrix_1.4-1             XML_3.99-0.9             pkgconfig_2.0.3         
[22] genefilter_1.78.0        zlibbioc_1.42.0          xtable_1.8-4            
[25] purrr_0.3.4              scales_1.2.0             BiocParallel_1.30.2     
[28] annotate_1.74.0          tibble_3.1.7             KEGGREST_1.36.0         
[31] generics_0.1.2           ggplot2_3.3.6            ellipsis_0.3.2          
[34] withr_2.5.0              cachem_1.0.6             GenomicFeatures_1.48.1  
[37] cli_3.3.0                survival_3.3-1           magrittr_2.0.3          
[40] crayon_1.5.1             memoise_2.0.1            fansi_1.0.3             
[43] xml2_1.3.3               tools_4.2.0              prettyunits_1.1.1       
[46] hms_1.1.1                BiocIO_1.6.0             lifecycle_1.0.1         
[49] stringr_1.4.0            locfit_1.5-9.5           munsell_0.5.0           
[52] DelayedArray_0.22.0      Biostrings_2.64.0        compiler_4.2.0          
[55] rlang_1.0.2              grid_4.2.0               RCurl_1.98-1.6          
[58] rstudioapi_0.13          rjson_0.2.21             rappdirs_0.3.3          
[61] bitops_1.0-7             restfulr_0.0.13          gtable_0.3.0            
[64] DBI_1.1.2                curl_4.3.2               R6_2.5.1                
[67] GenomicAlignments_1.32.0 dplyr_1.0.9              rtracklayer_1.56.0      
[70] fastmap_1.1.0            bit_4.0.4                utf8_1.2.2              
[73] filelock_1.0.2           stringi_1.7.6            parallel_4.2.0          
[76] Rcpp_1.0.8.3             geneplotter_1.74.0       vctrs_0.4.1             
[79] png_0.1-7                dbplyr_2.1.1             tidyselect_1.1.2