biomaRt connection error
2
0
Entering edit mode
ATpoint ▴ 870
@atpoint-13662
Last seen 29 minutes 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 • 191 views
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1
Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 26 minutes ago
EMBL Heidelberg / de.NBI

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

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0
Entering edit mode
@james-w-macdonald-5106
Last seen 22 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        
>

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