Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
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0
Entering edit mode
Lan Anh • 0
@48026bbb
Last seen 4 weeks ago
Japan

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   
biomaRt AnnotationForge • 232 views
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Entering edit mode

I'm not able to reproduce this. Maybe it was a temporary issue with biomaRt?

>  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
+     )
preparing data from NCBI ...
starting download for 
[1] gene2pubmed.gz
[2] gene2accession.gz
[3] gene2refseq.gz
[4] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
extracting data for our organism from : gene_info
getting data for gene2go.gz
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Please be patient while we work out which organisms can be annotated
  with ensembl IDs.
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
making the OrgDb package ...
Populating genes table:
genes table filled
Populating pubmed table:
pubmed table filled
Populating chromosomes table:
chromosomes table filled
Populating gene_info table:
gene_info table filled
Populating entrez_genes table:
entrez_genes table filled
Populating alias table:
alias table filled
Populating refseq table:
refseq table filled
Populating accessions table:
accessions table filled
Populating go table:
go table filled
table metadata filled

'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in /home/shepherd/Projects/RandomWorkNotes/AnnotationInstanceStuff/NonStandardOrg/org.Spombe.eg.db 
Now deleting temporary database file
complete!
[1] "org.Spombe.eg.sqlite"

Could you try making sure all the packages are up-to-date by running BiocManager::valid() and try again?

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0
Entering edit mode

Hello,

Sorry for the late answer, I called several packages after my error and I do not know how it worked after that. Thank you for the help!

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