Error(s) in re-building vignettes:
  ...
--- re-building ‘a_introduction.Rmd’ using rmarkdown
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Using 'subset' is not compatible the @results table.
Alert: Using 'subset' disables permutation testing.
Alert: Using 'subset' is not compatible the @results table.
Alert: Using 'subset' disables permutation testing.
Quitting from lines 102-103 (a_introduction.Rmd) 
Error: processing vignette 'a_introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘a_introduction.Rmd’

--- re-building ‘b_visualization.Rmd’ using rmarkdown
Quitting from lines 60-61 (b_visualization.Rmd) 
Error: processing vignette 'b_visualization.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘b_visualization.Rmd’

--- re-building ‘d_advanced.Rmd’ using rmarkdown
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
--- finished re-building ‘d_advanced.Rmd’

--- re-building ‘e_differential.Rmd’ using rmarkdown
Alert: Fixing permutations to active random seed.
Alert: Use 'setActive' to select a theta type.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Use 'updateF' to calculate F-stat.
Alert: Update FDR or F-stat manually.
Alert: Update FDR or F-stat manually.
Quitting from lines 180-181 (e_differential.Rmd) 
Error: processing vignette 'e_differential.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘e_differential.Rmd’

--- re-building ‘f_moderation.Rmd’ using rmarkdown
Alert: Fixing permutations to active random seed.
Alert: Use 'setActive' to select a theta type.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Use 'updateF' to calculate F-stat.
--- finished re-building ‘f_moderation.Rmd’

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

SUMMARY: processing the following files failed:
  ‘a_introduction.Rmd’ ‘b_visualization.Rmd’ ‘e_differential.Rmd’

Error: Vignette re-building failed.
Execution halted