Error(s) in re-building vignettes:
--- re-building 'RRphylo.Rmd' using rmarkdown
Loading required package: ape
Loading required package: kableExtra
Quitting from lines 53-72 (RRphylo.Rmd) 
Error: processing vignette 'RRphylo.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'RRphylo.Rmd'

--- re-building 'Tree-Manipulation.Rmd' using rmarkdown
Loading required package: ape
Loading required package: phytools
Loading required package: maps
Loading required package: geiger
Loading required package: kableExtra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Quitting from lines 52-73 (Tree-Manipulation.Rmd) 
Error: processing vignette 'Tree-Manipulation.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'Tree-Manipulation.Rmd'

--- re-building 'overfitRR.Rmd' using rmarkdown
Loading required package: RRphylo
Loading required package: emmeans
--- finished re-building 'overfitRR.Rmd'

--- re-building 'search.conv.Rmd' using rmarkdown
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: kableExtra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Quitting from lines 545-610 (search.conv.Rmd) 
Error: processing vignette 'search.conv.Rmd' failed with diagnostics:
could not find function "row_spec"
--- failed re-building 'search.conv.Rmd'

--- re-building 'search.shift.Rmd' using rmarkdown
Loading required package: ape
Loading required package: phytools
Loading required package: maps
Loading required package: geiger
Loading required package: scales

Attaching package: 'scales'

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

    rescale

is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: kableExtra
Quitting from lines 41-102 (search.shift.Rmd) 
Error: processing vignette 'search.shift.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'search.shift.Rmd'

--- re-building 'search.trend.Rmd' using rmarkdown
Loading required package: ape
Loading required package: geiger
Loading required package: phytools
Loading required package: maps
Loading required package: ddpcr

Attaching package: 'ddpcr'

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

    step

is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Quitting from lines 37-196 (search.trend.Rmd) 
Error: processing vignette 'search.trend.Rmd' failed with diagnostics:
Package "car" needed for this function to work. Please install it.
--- failed re-building 'search.trend.Rmd'

--- re-building 'swapONE.Rmd' using rmarkdown
Loading required package: ape
Loading required package: phytools
Loading required package: maps
Loading required package: geiger
--- finished re-building 'swapONE.Rmd'

SUMMARY: processing the following files failed:
  'RRphylo.Rmd' 'Tree-Manipulation.Rmd' 'search.conv.Rmd'
  'search.shift.Rmd' 'search.trend.Rmd'

Error: Vignette re-building failed.
Execution halted