Error(s) in re-building vignettes:
--- re-building 'myTAI.Rmd' using rmarkdown
--- finished re-building 'myTAI.Rmd'

--- re-building 'other-strata.Rmd' using rmarkdown
--- finished re-building 'other-strata.Rmd'

--- re-building 'phylo-expression-object.Rmd' using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building 'phylo-expression-object.Rmd'

--- re-building 'phylostratigraphy.Rmd' using rmarkdown
--- finished re-building 'phylostratigraphy.Rmd'

--- re-building 'tai-breaker.Rmd' using rmarkdown
--- finished re-building 'tai-breaker.Rmd'

--- re-building 'tai-gallery.Rmd' using rmarkdown
--- finished re-building 'tai-gallery.Rmd'

--- re-building 'tai-stats.Rmd' using rmarkdown
--- finished re-building 'tai-stats.Rmd'

--- re-building 'tai-transform.Rmd' using rmarkdown
--- finished re-building 'tai-transform.Rmd'

--- re-building 'taxonomy.Rmd' using rmarkdown

Quitting from taxonomy.Rmd:307-311 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Gateway Timeout (HTTP 504)
---
Backtrace:
     ▆
  1. └─global taxonomy(organism = "Arabidopsis", db = "itis", output = "children")
  2.   ├─base::as.data.frame(taxize::children(organism, db = db)[[1]])
  3.   ├─taxize::children(organism, db = db)
  4.   └─taxize:::children.default(organism, db = db)
  5.     ├─stats::setNames(children(id, ...), sci_id)
  6.     ├─taxize::children(id, ...)
  7.     └─taxize:::children.tsn(id, ...)
  8.       └─base::lapply(sci_id, fun)
  9.         └─taxize (local) FUN(X[[i]], ...)
 10.           └─ritis::hierarchy_down(y, ...)
 11.             └─ritis:::itis_GET(...)
 12.               └─tt$raise_for_status()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
Gateway Timeout (HTTP 504)
--- failed re-building 'taxonomy.Rmd'

SUMMARY: processing the following file failed:
  'taxonomy.Rmd'

Error: Vignette re-building failed.
Execution halted