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

--- finished 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


Attaching package: 'ggridges'

The following object is masked from 'package:ggplot2':

    scale_discrete_manual

Picking joint bandwidth of 0.0248
--- finished re-building 'CRM-visualisation.Rmd'

--- re-building 'CRM.Rmd' using rmarkdown
Loading required package: Rcpp
Warning: There were 1 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
Quitting from lines 235-240 (EffTox.Rmd) 
Error: processing vignette 'EffTox.Rmd' failed with diagnostics:
there is no package called 'bcrm'
--- failed re-building 'EffTox.Rmd'

--- re-building 'HierarchicalBayesianResponse.Rmd' using rmarkdown
Loading required package: Rcpp
Loading required package: StanHeaders
rstan (Version 2.19.2, 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)
For improved execution time, we recommend calling
Sys.setenv(LOCAL_CPPFLAGS = '-march=native')
although this causes Stan to throw an error on a few processors.

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 2092 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 2042 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 2060 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 2090 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: There were 2087 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 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: `cols` is now required.
Please use `cols = c(Dose, ProbTox)`
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

Warning: `cols` is now required.
Please use `cols = c(Dose, ProbTox)`
--- 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 file failed:
  'EffTox.Rmd'

Error: Vignette re-building failed.
Execution halted