annotaR

package dependencies

Package required but not available: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

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re-building of vignette outputs

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 10014 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(http_config = list())
 12.             └─biomaRt:::.checkArchiveList(http_config)
 13.               └─biomaRt:::.getArchiveList(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 10014 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

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