Error(s) in re-building vignettes:
  ...
--- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 84-119 (AminoAcids-Vignette.Rmd) 
Error: processing vignette 'AminoAcids-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘AminoAcids-Vignette.Rmd’

--- re-building ‘Diversity-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 112-115 (Diversity-Vignette.Rmd) 
Error: processing vignette 'Diversity-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Diversity-Vignette.Rmd’

--- re-building ‘GeneUsage-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in mutate_impl(.data, dots, caller_env()) :
  Unequal factor levels: coercing to character
Warning in mutate_impl(.data, dots, caller_env()) :
  binding character and factor vector, coercing into character vector
Warning in mutate_impl(.data, dots, caller_env()) :
  binding character and factor vector, coercing into character vector
Quitting from lines 84-100 (GeneUsage-Vignette.Rmd) 
Error: processing vignette 'GeneUsage-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GeneUsage-Vignette.Rmd’

--- re-building ‘Lineage-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'dplyr'

The following objects are masked from 'package:igraph':

    as_data_frame, groups, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘Lineage-Vignette.Rmd’

--- re-building ‘Topology-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'dplyr'

The following objects are masked from 'package:igraph':

    as_data_frame, groups, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 186-208 (Topology-Vignette.Rmd) 
Error: processing vignette 'Topology-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Topology-Vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘AminoAcids-Vignette.Rmd’ ‘Diversity-Vignette.Rmd’
  ‘GeneUsage-Vignette.Rmd’ ‘Topology-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted