Error(s) in re-building vignettes:
--- re-building 'Baseline-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
--- finished re-building 'Baseline-Vignette.Rmd'

--- re-building 'DistToNearest-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
--- finished re-building 'DistToNearest-Vignette.Rmd'

--- re-building 'Mutation-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.

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

--- finished re-building 'Mutation-Vignette.Rmd'

--- re-building 'Shmulate-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

--- finished re-building 'Shmulate-Vignette.Rmd'

--- re-building 'Targeting-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
Warning in createMutabilityMatrix(db, sub_mat, model = model, sequenceColumn = sequenceColumn,  :
  Insufficient number of mutations to infer some 5-mers. Filled with 0. 
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Quitting from lines 168-171 (Targeting-Vignette.Rmd) 
Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics:
replacement has 3 rows, data has 5
--- failed re-building 'Targeting-Vignette.Rmd'

SUMMARY: processing the following file failed:
  'Targeting-Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted