Error(s) in re-building vignettes:
  ...
--- re-building ‘annotaR-workflow.Rmd’ using rmarkdown

Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.processResults()`:
! Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
---
Backtrace:
    ▆
 1. ├─... %>% add_drug_links()
 2. ├─annotaR::add_drug_links(.)
 3. │ └─"gene" %in% names(annotaR_object)
 4. └─annotaR::add_disease_links(.)
 5.   └─biomaRt::getBM(...)
 6.     └─biomaRt:::.processResults(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics:
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

--- failed re-building ‘annotaR-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘annotaR-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘annotaR-workflow.Rmd’ using rmarkdown

Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.processResults()`:
! Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
---
Backtrace:
    ▆
 1. ├─... %>% add_drug_links()
 2. ├─annotaR::add_drug_links(.)
 3. │ └─"gene" %in% names(annotaR_object)
 4. └─annotaR::add_disease_links(.)
 5.   └─biomaRt::getBM(...)
 6.     └─biomaRt:::.processResults(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics:
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

--- failed re-building ‘annotaR-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘annotaR-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘annotaR-workflow.Rmd’ using rmarkdown

Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_failure>
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]:
Operation timed out after 10002 milliseconds with 0 bytes received
---
Backtrace:
     ▆
  1. ├─... %>% add_drug_links()
  2. ├─annotaR::add_drug_links(.)
  3. │ └─"gene" %in% names(annotaR_object)
  4. └─annotaR::add_disease_links(.)
  5.   └─biomaRt::getBM(...)
  6.     └─biomaRt:::.createHash(...)
  7.       └─biomaRt:::.listEnsemblArchives(http_config = martHTTPConfig(mart))
  8.         └─biomaRt:::.checkArchiveList(http_config)
  9.           └─biomaRt:::.getArchiveList(http_config = http_config)
 10.             └─httr2::req_perform(html_request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]:
Operation timed out after 10002 milliseconds with 0 bytes received
--- failed re-building ‘annotaR-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘annotaR-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'annotaR-workflow.Rmd' using rmarkdown

Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_failure>
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]:
Operation timed out after 10012 milliseconds with 0 bytes received
---
Backtrace:
     ▆
  1. ├─... %>% add_drug_links()
  2. ├─annotaR::add_drug_links(.)
  3. │ └─"gene" %in% names(annotaR_object)
  4. └─annotaR::add_disease_links(.)
  5.   ├─biomaRt::getBM(...)
  6.   │ └─biomaRt:::martCheck(mart)
  7.   └─biomaRt::useEnsembl("genes", "hsapiens_gene_ensembl")
  8.     └─biomaRt:::.listEnsembl(version = version, GRCh = GRCh, mirror = mirror)
  9.       └─biomaRt:::.currentEnsemblVersion()
 10.         └─biomaRt::listEnsemblArchives()
 11.           └─biomaRt:::.listEnsemblArchives(https = https, http_config = list())
 12.             └─biomaRt:::.checkArchiveList(https, http_config)
 13.               └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
 14.                 └─httr2::req_perform(html_request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]:
Operation timed out after 10012 milliseconds with 0 bytes received
--- failed re-building 'annotaR-workflow.Rmd'

SUMMARY: processing the following file failed:
  'annotaR-workflow.Rmd'

Error: Vignette re-building failed.
Execution halted