Error(s) in re-building vignettes:
--- re-building ‘bayesdfa.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: StanHeaders
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
Warning: There were 1 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Not enough tail samples to fit the generalized Pareto distribution in some or all columns of matrix of log importance ratios. Skipping the following columns: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... [70 more not printed].

Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.

Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
--- finished re-building ‘bayesdfa.Rmd’

--- re-building ‘combining_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: StanHeaders
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Warning in 1:(idx - 1) :
  numerical expression has 3 elements: only the first used
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning in 1:(idx - 1) :
  numerical expression has 3 elements: only the first used
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning in 1:(idx - 1) :
  numerical expression has 3 elements: only the first used
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
--- finished re-building ‘combining_data.Rmd’

--- re-building ‘compositional.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: StanHeaders
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is 1.9, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
http://mc-stan.org/misc/warnings.html#bfmi-low
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is 1.9, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
--- finished re-building ‘compositional.Rmd’

--- re-building ‘covariates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: StanHeaders
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

--- finished re-building ‘covariates.Rmd’

--- re-building ‘estimate_process_sigma.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: StanHeaders
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Warning: There were 5 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
Warning: There were 3 divergent transitions after warmup. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
http://mc-stan.org/misc/warnings.html#bfmi-low
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
error occurred during calling the sampler; sampling not done
Quitting from lines 95-101 (estimate_process_sigma.Rmd) 
Error: processing vignette 'estimate_process_sigma.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘estimate_process_sigma.Rmd’

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

Error: Vignette re-building failed.
Execution halted