Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
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Svitlana ▴ 10
@725810d7
Last seen 27 days ago
United States

Hi, I am having issues with retrieving mouse SNP dataset, could you please fix it?

ensembl <- useEnsembl(biomart = "snps", dataset = "mmusculus_snp")

Error in .getFilters(mart, verbose = verbose) : 
  biomaRt error: looks like we're connecting to incompatible version of BioMart.

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

other attached packages:
[1] biomaRt_2.60.0

loaded via a namespace (and not attached):
 [1] rappdirs_0.3.3          utf8_1.2.4              generics_0.1.3         
 [4] xml2_1.3.6              RSQLite_2.3.7           stringi_1.8.4          
 [7] hms_1.1.3               digest_0.6.35           magrittr_2.0.3         
[10] fastmap_1.2.0           blob_1.2.4              jsonlite_1.8.8         
[13] progress_1.2.3          AnnotationDbi_1.66.0    GenomeInfoDb_1.40.1    
[16] DBI_1.2.3               BiocManager_1.30.23     httr_1.4.7             
[19] purrr_1.0.2             fansi_1.0.6             UCSC.utils_1.0.0       
[22] Biostrings_2.72.1       httr2_1.0.1             cli_3.6.2              
[25] rlang_1.1.3             crayon_1.5.2            dbplyr_2.5.0           
[28] XVector_0.44.0          Biobase_2.64.0          bit64_4.0.5            
[31] withr_3.0.0             cachem_1.1.0            tools_4.4.0            
[34] memoise_2.0.1           dplyr_1.1.4             GenomeInfoDbData_1.2.12
[37] filelock_1.0.3          BiocGenerics_0.50.0     curl_5.2.1             
[40] vctrs_0.6.5             R6_2.5.1                png_0.1-8              
[43] stats4_4.4.0            lifecycle_1.0.4         BiocFileCache_2.12.0   
[46] zlibbioc_1.50.0         KEGGREST_1.44.0         stringr_1.5.1          
[49] S4Vectors_0.42.0        IRanges_2.38.0          bit_4.0.5              
[52] pkgconfig_2.0.3         pillar_1.9.0            glue_1.7.0             
[55] tibble_3.2.1            tidyselect_1.2.1        compiler_4.4.0         
[58] prettyunits_1.2.0
biomaRt • 631 views
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Thank you so much! The issue has been resolved.

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Mike Smith ★ 6.5k
@mike-smith
Last seen 8 hours ago
EMBL Heidelberg

Thank you for reporting this. There seemed to be an issue where the list of available filters returned by the BioMart server when using the SNP data set was using a different character encoding to what the package was expecting. This only seemed to affect that particular data set.

I've patched the package and it should work now. This is available in version 2.60.1, which will become available via Bioconductor in a few days. You can installed immediately from GitHub via:

BiocManager::install('grimbough/biomaRt', ref = "v2.60.1")
> useEnsembl(biomart = "snps", dataset = "mmusculus_snp")
Object of class 'Mart':
  Using the ENSEMBL_MART_SNP BioMart database
  Using the mmusculus_snp dataset
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