Package check result: OK

Changes to worse in reverse depends:

Package: annotaR
Check: re-building of vignette outputs
New result: ERROR
  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