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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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

Quitting from gemma.R.Rmd:88-109 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'head': Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─... %>% gemma_kable
  2. ├─gemma.R::gemma_kable(.)
  3. │ └─base::ncol(table)
  4. ├─utils::head(.)
  5. ├─dplyr::select(...)
  6. ├─gemma.R::get_datasets(taxa = c("mouse", "human"))
  7. │ └─gemma.R:::memget_datasets(...)
  8. │   ├─gemma.R (local) mem_call(...)
  9. │   │ ├─base::withVisible(eval(mc, parent.frame()))
 10. │   │ └─base::eval(mc, parent.frame())
 11. │   │   └─base::eval(mc, parent.frame())
 12. │   └─gemma.R (local) `<fn>`(...)
 13. │     └─gemma.R:::.body(...)
 14. │       ├─base::eval(requestExpr)
 15. │       │ └─base::eval(requestExpr)
 16. │       └─httr::GET(...)
 17. │         └─httr:::request_perform(req, hu$handle$handle)
 18. │           ├─httr:::request_fetch(req$output, req$url, handle)
 19. │           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 20. │             └─curl::curl_fetch_memory(url, handle = handle)
 21. ├─curl:::raise_libcurl_error(...)
 22. │ └─base::stop(e)
 23. └─base (local) `<fn>`(`<crl_rr__>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'head': Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
--- failed 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:468-484 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─gemma.R::get_dataset_object(...)
  2. │ └─unique_sets %>% ...
  3. ├─base::lapply(...)
  4. │ └─gemma.R (local) FUN(X[[i]], ...)
  5. │   └─gemma.R::get_dataset_samples(dataset, memoised = memoised)
  6. │     └─gemma.R:::memget_dataset_samples(...)
  7. │       ├─gemma.R (local) mem_call(...)
  8. │       │ ├─base::withVisible(eval(mc, parent.frame()))
  9. │       │ └─base::eval(mc, parent.frame())
 10. │       │   └─base::eval(mc, parent.frame())
 11. │       └─gemma.R (local) `<fn>`(...)
 12. │         └─gemma.R:::.body(...)
 13. │           ├─base::eval(requestExpr)
 14. │           │ └─base::eval(requestExpr)
 15. │           └─httr::GET(...)
 16. │             └─httr:::request_perform(req, hu$handle$handle)
 17. │               ├─httr:::request_fetch(req$output, req$url, handle)
 18. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 19. │                 └─curl::curl_fetch_memory(url, handle = handle)
 20. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
Timeout was reached [gemma.msl.ubc.ca]:
SSL connection timeout
--- failed re-building ‘metanalysis.Rmd’

SUMMARY: processing the following files failed:
  ‘gemma.R.Rmd’ ‘metanalysis.Rmd’

Error: Vignette re-building failed.
Execution halted