Error(s) in re-building vignettes:
  ...
--- re-building 'BEBOP.Rmd' using rmarkdown
Loading required package: Rcpp
ci_level: 0.8 (80% intervals)
outer_level: 0.95 (95% intervals)
--- finished re-building 'BEBOP.Rmd'

--- re-building 'CRM-pathways.Rmd' using rmarkdown
Loading required package: Rcpp

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

New names:
* `` -> ...1
* `` -> ...2
* `` -> ...3
* `` -> ...4
* `` -> ...5
Quitting from lines 128-136 (CRM-pathways.Rmd) 
Error: processing vignette 'CRM-pathways.Rmd' failed with diagnostics:
Assigned data `draws[, c(".chain", ".iteration", ".draw")]` must be compatible with existing data.
x Existing data has 20000 rows.
x Element 1 of assigned data has 4000 rows.
i Only vectors of size 1 are recycled.
--- failed re-building 'CRM-pathways.Rmd'

--- re-building 'CRM-visualisation.Rmd' using rmarkdown
Loading required package: Rcpp

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 61-68 (CRM-visualisation.Rmd) 
Error: processing vignette 'CRM-visualisation.Rmd' failed with diagnostics:
Assigned data `draws[, c(".chain", ".iteration", ".draw")]` must be compatible with existing data.
x Existing data has 20000 rows.
x Element 1 of assigned data has 4000 rows.
i Only vectors of size 1 are recycled.
--- failed re-building 'CRM-visualisation.Rmd'

--- re-building 'CRM.Rmd' using rmarkdown
Loading required package: Rcpp
Warning: There were 3 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

--- finished re-building 'CRM.Rmd'

--- re-building 'EffTox.Rmd' using rmarkdown
Loading required package: Rcpp
--- finished re-building 'EffTox.Rmd'

--- re-building 'HierarchicalBayesianResponse.Rmd' using rmarkdown
Loading required package: Rcpp
Loading required package: StanHeaders
rstan (Version 2.19.3, 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)

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

ci_level: 0.8 (80% intervals)
outer_level: 0.95 (95% intervals)
--- finished re-building 'HierarchicalBayesianResponse.Rmd'

--- re-building 'LevyCaseStudy.Rmd' using rmarkdown

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: There were 2023 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
Warning: There were 2062 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
Warning: There were 1964 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
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: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
Warning: There were 2051 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: There were 1953 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: There were 2079 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: There were 2020 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: There were 185 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 66 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 17 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 5 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.99 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

--- finished re-building 'LevyCaseStudy.Rmd'

--- re-building 'TITE-CRM.Rmd' using rmarkdown
Loading required package: Rcpp
--- finished re-building 'TITE-CRM.Rmd'

SUMMARY: processing the following files failed:
  'CRM-pathways.Rmd' 'CRM-visualisation.Rmd'

Error: Vignette re-building failed.
Execution halted