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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R
###
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* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown
Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘gemma.R.Rmd’

--- re-building ‘metadata.Rmd’ using rmarkdown
--- finished re-building ‘metadata.Rmd’

--- re-building ‘metanalysis.Rmd’ using rmarkdown

Quitting from metanalysis.Rmd:225-238 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [gemma.msl.ubc.ca]: Connection timed out after 10001 milliseconds
---
Backtrace:
     ▆
  1. ├─parkin_contrasts$result.ID %>% ...
  2. ├─BiocGenerics::lapply(...)
  3. ├─base::lapply(...)
  4. │ └─FUN(X[[i]], ...)
  5. │   └─gemma.R::get_differential_expression_values(resultSets = x)
  6. │     └─base::lapply(...)
  7. │       └─gemma.R (local) FUN(X[[i]], ...)
  8. │         └─gemma.R:::.getResultSets(x, memoised = memoised)
  9. │           └─gemma.R:::mem.getResultSets(...)
 10. │             ├─gemma.R (local) mem_call(...)
 11. │             │ ├─base::withVisible(eval(mc, parent.frame()))
 12. │             │ └─base::eval(mc, parent.frame())
 13. │             │   └─base::eval(mc, parent.frame())
 14. │             └─gemma.R (local) `<fn>`(...)
 15. │               ├─gemma.R:::.body(...)
 16. │               │ └─base::eval(requestExpr, envir = envWhere)
 17. │               │   └─base::eval(requestExpr, envir = envWhere)
 18. │               └─httr::GET(...)
 19. │                 └─httr:::request_perform(req, hu$handle$handle)
 20. │                   ├─httr:::request_fetch(req$output, req$url, handle)
 21. │                   └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 22. │                     └─curl::curl_fetch_memory(url, handle = handle)
 23. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
Timeout was reached [gemma.msl.ubc.ca]: Connection timed out after 10001 milliseconds
--- failed re-building ‘metanalysis.Rmd’

SUMMARY: processing the following file failed:
  ‘metanalysis.Rmd’

Error: Vignette re-building failed.
Execution halted