Ensembl site unresponsive, trying uswest mirror
1
0
Entering edit mode
@16215245
Last seen 2.5 years ago
Hungary

Some one help me understand why I can not successfully access ensembl webpage

Code should be placed in three backticks as shown below

ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="oaries_gene_ensembl")

The above script gives the output below

Ensembl site unresponsive, trying uswest mirror

Results of running the following in an R session

sessionInfo( )

sessionInfo() ```R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 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] qqman_0.1.8 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[6] readr_2.0.2 tidyr_1.1.4 tibble_3.1.2 ggplot2_3.3.5 tidyverse_1.3.1 [11] biomaRt_2.48.3

loaded via a namespace (and not attached): [1] Biobase_2.52.0 httr_1.4.2 vroom_1.5.5
[4] bit64_4.0.5 jsonlite_1.7.2 modelr_0.1.8
[7] assertthat_0.2.1 BiocManager_1.30.16 stats4_4.1.0
[10] BiocFileCache_2.0.0 blob_1.2.2 GenomeInfoDbData_1.2.6 [13] cellranger_1.1.0 progress_1.2.2 pillar_1.6.4
[16] RSQLite_2.2.8 backports_1.2.1 glue_1.4.2
[19] digest_0.6.28 XVector_0.32.0 rvest_1.0.2
[22] colorspace_2.0-2 XML_3.99-0.8 pkgconfig_2.0.3
[25] broom_0.7.10 haven_2.4.3 calibrate_1.7.7
[28] zlibbioc_1.38.0 scales_1.1.1 tzdb_0.1.2
[31] KEGGREST_1.32.0 generics_0.1.1 IRanges_2.26.0
[34] ellipsis_0.3.2 withr_2.4.2 cachem_1.0.6
[37] BiocGenerics_0.38.0 cli_3.0.0 magrittr_2.0.1
[40] crayon_1.4.2 readxl_1.3.1 memoise_2.0.0
[43] fs_1.5.0 fansi_0.5.0 MASS_7.3-54
[46] xml2_1.3.2 tools_4.1.0 prettyunits_1.1.1
[49] hms_1.1.1 lifecycle_1.0.1 S4Vectors_0.30.2
[52] munsell_0.5.0 reprex_2.0.1 AnnotationDbi_1.54.1
[55] Biostrings_2.60.2 compiler_4.1.0 GenomeInfoDb_1.28.4
[58] rlang_0.4.11 grid_4.1.0 RCurl_1.98-1.5
[61] rstudioapi_0.13 rappdirs_0.3.3 bitops_1.0-7
[64] gtable_0.3.0 DBI_1.1.1 curl_4.3.2
[67] R6_2.5.1 lubridate_1.8.0 fastmap_1.1.0
[70] bit_4.0.4 utf8_1.2.1 filelock_1.0.2
[73] stringi_1.7.5 parallel_4.1.0 Rcpp_1.0.7
[76] vctrs_0.3.8 png_0.1-7 dbplyr_2.1.1
[79] tidyselect_1.1.1```

GenomicVariantsWorkflow • 4.2k views
ADD COMMENT
0
Entering edit mode

Hi Geog,

I had the same issue and the suggestion was to upgrade to new version of Bioconductor. After upgrade it worked fine but again today I am facing the same issue

ADD REPLY
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

Try useEnsembl instead.

> mart <- useEnsembl("ensembl","oaries_gene_ensembl")
> mart
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the oaries_gene_ensembl dataset> 
> sessionInfo()
R version 4.1.0 (2021-05-18)
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_4.1.0           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_1.4.2             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_1.56.0   fansi_0.5.0           
[34] Rcpp_1.0.7             filelock_1.0.2         cachem_1.0.6          
[37] S4Vectors_0.32.0       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_4.1.0           
[46] bitops_1.0-7           magrittr_2.0.1         RCurl_1.98-1.5        
[49] RSQLite_2.2.8          tibble_3.1.5           crayon_1.4.1          
[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] rstudioapi_0.13        R6_2.5.1               compiler_4.1.0
ADD COMMENT

Login before adding your answer.

Traffic: 470 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