Error(s) in re-building vignettes:
  ...
--- re-building ‘myTAI.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘myTAI.Rmd’

--- re-building ‘other-strata.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phylo-expression-object.Rmd’

--- re-building ‘phylostratigraphy.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phylostratigraphy.Rmd’

--- re-building ‘tai-breaker.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-breaker.Rmd’

--- re-building ‘tai-gallery.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-gallery.Rmd’

--- re-building ‘tai-stats.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-stats.Rmd’

--- re-building ‘tai-transform.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-transform.Rmd’

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

Quitting from taxonomy.Rmd:225-229 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dplyr::filter()`:
ℹ In argument: `name == organism`.
Caused by error:
! `..1` must be of size 1, not size 0.
---
Backtrace:
     ▆
  1. ├─global taxonomy(organism = "Arabidopsis thaliana", db = "ncbi", output = "taxid")
  2. │ ├─dplyr::select(...)
  3. │ ├─dplyr::filter(tax_hierarchy, name == organism)
  4. │ └─dplyr:::filter.data.frame(tax_hierarchy, name == organism)
  5. │   └─dplyr:::filter_rows(.data, dots, by)
  6. │     └─dplyr:::filter_eval(...)
  7. │       ├─base::withCallingHandlers(...)
  8. │       └─mask$eval_all_filter(dots, env_filter)
  9. │         └─dplyr (local) eval()
 10. └─dplyr:::dplyr_internal_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
ℹ In argument: `name == organism`.
Caused by error:
! `..1` must be of size 1, not size 0.
--- failed re-building ‘taxonomy.Rmd’

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

Error: Vignette re-building failed.
Execution halted