biomaRt connection error
2
0
Entering edit mode
ATpoint ★ 4.6k
@atpoint-13662
Last seen 4 hours ago
Germany

Any idea what is going on here?

library(biomaRt)
mart = useEnsembl("genes", dataset = "mmusculus_gene_ensembl", version=100)

probe2gene <- getBM(attributes=c("affy_mouse430_2", "ensembl_gene_id", "mgi_symbol"), 
                    mart=mart)

Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery,  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_100: DBI connect('database=ensembl_mart_100;host=hh-mysql-ens-archive-mart-web;port=4566','ensro',...) failed: Can't connect to MySQL server on 'hh-mysql-ens-archive-mart-web' (113) at /nfs/public/ro/ensweb/live/archive/www/e100/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.



R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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    parallel  stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] biomaRt_2.46.1       pd.mouse430.2_3.12.0 DBI_1.1.1            RSQLite_2.2.3        oligo_1.54.1         Biostrings_2.58.0   
 [7] XVector_0.30.0       IRanges_2.24.1       S4Vectors_0.28.1     oligoClasses_1.52.0  GEOquery_2.58.0      Biobase_2.50.0      
[13] BiocGenerics_0.36.0  forcats_0.5.1        stringr_1.4.0        dplyr_1.0.5          purrr_0.3.4          readr_1.4.0         
[19] tidyr_1.1.3          tibble_3.1.1         tidyverse_1.3.1      limma_3.46.0         ggplot2_3.3.3        RhpcBLASctl_0.20-137
[25] rprojroot_2.0.2      rmarkdown_2.11       knitr_1.30          

loaded via a namespace (and not attached):
 [1] colorspace_2.0-0            ellipsis_0.3.1              GenomicRanges_1.42.0        fs_1.5.0                   
 [5] rstudioapi_0.13             affyio_1.60.0               ggrepel_0.9.1               bit64_4.0.5                
 [9] AnnotationDbi_1.52.0        fansi_0.4.2                 lubridate_1.8.0             xml2_1.3.2                 
[13] codetools_0.2-18            splines_4.0.3               sparseMatrixStats_1.2.0     cachem_1.0.1               
[17] jsonlite_1.7.2              broom_0.7.9                 dbplyr_2.1.1                BiocManager_1.30.10        
[21] compiler_4.0.3              httr_1.4.2                  dqrng_0.2.1                 backports_1.2.1            
[25] assertthat_0.2.1            Matrix_1.3-2                fastmap_1.1.0               cli_2.4.0                  
[29] BiocSingular_1.6.0          prettyunits_1.1.1           htmltools_0.5.1.1           tools_4.0.3                
[33] rsvd_1.0.3                  igraph_1.2.6                gtable_0.3.0                glue_1.4.2                 
[37] GenomeInfoDbData_1.2.4      reshape2_1.4.4              affxparser_1.62.0           rappdirs_0.3.1             
[41] Rcpp_1.0.6                  cellranger_1.1.0            vctrs_0.3.6                 preprocessCore_1.52.1      
[45] iterators_1.0.13            DelayedMatrixStats_1.12.2   xfun_0.24                   beachmat_2.6.4             
[49] rvest_1.0.1                 lifecycle_1.0.0             irlba_2.3.3                 renv_0.13.2                
[53] PCAtools_2.2.0              XML_3.99-0.5                zlibbioc_1.36.0             scales_1.1.1               
[57] hms_1.0.0                   MatrixGenerics_1.2.0        SummarizedExperiment_1.20.0 yaml_2.2.1                 
[61] curl_4.3                    memoise_2.0.0               stringi_1.5.3               vizzy_1.2.1                
[65] foreach_1.5.1               BiocParallel_1.24.1         GenomeInfoDb_1.26.2         rlang_0.4.10               
[69] pkgconfig_2.0.3             matrixStats_0.57.0          bitops_1.0-6                evaluate_0.14              
[73] lattice_0.20-41             cowplot_1.1.1               bit_4.0.4                   tidyselect_1.1.0           
[77] plyr_1.8.6                  magrittr_2.0.1              R6_2.5.0                    generics_0.1.0             
[81] DelayedArray_0.16.1         pillar_1.6.0                haven_2.4.3                 withr_2.4.2                
[85] RCurl_1.98-1.2              modelr_0.1.8                crayon_1.4.1                utf8_1.1.4                 
[89] BiocFileCache_1.14.0        progress_1.2.2              grid_4.0.3                  readxl_1.3.1               
[93] blob_1.2.1                  reprex_2.0.1                digest_0.6.27               ff_4.0.4                   
[97] openssl_1.4.3               munsell_0.5.0               askpass_1.1                
biomaRt • 1.2k views
ADD COMMENT
1
Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 1 hour ago
EMBL Heidelberg

Looks like Ensembl had some issues, which should now be sorted: https://www.ensembl.info/2021/11/18/temporary-disruption-to-ensembl-tools-2/

ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 12 hours ago
United States

Either

A.) you are using an outdated version of R/Bioc that doesn't work and you should upgrade

B.) it was a transitory problem, given the fact that you are making a query on the intertubes and things happen.

> mart = useEnsembl("genes", dataset = "mmusculus_gene_ensembl", version=100)
Warning message:
In listEnsemblArchives(https = FALSE) :
  Ensembl will soon enforce the use of https.
As such the 'https' argument will be deprecated in the next release.
> 
> probe2gene <- getBM(attributes=c("affy_mouse430_2", "ensembl_gene_id", "mgi_symbol"), 
+                     mart=mart)
> head(probe2gene)
  affy_mouse430_2    ensembl_gene_id mgi_symbol
1                 ENSMUSG00000064372      mt-Tp
2                 ENSMUSG00000064371      mt-Tt
3                 ENSMUSG00000064370    mt-Cytb
4                 ENSMUSG00000064369      mt-Te
5                 ENSMUSG00000064368     mt-Nd6
6      1426088_at ENSMUSG00000064367     mt-Nd5
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] 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] biomaRt_2.50.0

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.1      
 [4] purrr_0.3.4            vctrs_0.3.8            generics_0.1.1        
 [7] stats4_4.1.2           BiocFileCache_2.2.0    utf8_1.2.2            
[10] blob_1.2.2             XML_3.99-0.8           rlang_0.4.12          
[13] pillar_1.6.4           glue_1.5.0             withr_2.4.2           
[16] DBI_1.1.1              rappdirs_0.3.3         BiocGenerics_0.40.0   
[19] bit64_4.0.5            dbplyr_2.1.1           GenomeInfoDbData_1.2.7
[22] lifecycle_1.0.1        stringr_1.4.0          zlibbioc_1.40.0       
[25] Biostrings_2.62.0      memoise_2.0.0          Biobase_2.54.0        
[28] IRanges_2.28.0         fastmap_1.1.0          GenomeInfoDb_1.30.0   
[31] curl_4.3.2             AnnotationDbi_1.56.1   fansi_0.5.0           
[34] Rcpp_1.0.7             filelock_1.0.2         cachem_1.0.6          
[37] S4Vectors_0.32.2       XVector_0.34.0         bit_4.0.4             
[40] hms_1.1.1              png_0.1-7              digest_0.6.28         
[43] stringi_1.7.5          dplyr_1.0.7            tools_4.1.2           
[46] bitops_1.0-7           magrittr_2.0.1         RCurl_1.98-1.5        
[49] RSQLite_2.2.8          tibble_3.1.6           crayon_1.4.2          
[52] pkgconfig_2.0.3        ellipsis_0.3.2         xml2_1.3.2            
[55] prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.2            
[58] R6_2.5.1               compiler_4.1.2        
>
ADD COMMENT

Login before adding your answer.

Traffic: 828 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6