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```
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