Entering edit mode
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