Error(s) in re-building vignettes:
--- re-building 'A200-CRM.Rmd' using rmarkdown
Loading required package: Rcpp
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

--- finished re-building 'A200-CRM.Rmd'

--- re-building 'A210-CRM-visualisation.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


Attaching package: 'ggridges'

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

    scale_point_color_continuous, scale_point_color_discrete,
    scale_point_colour_continuous, scale_point_colour_discrete,
    scale_point_fill_continuous, scale_point_fill_discrete,
    scale_point_size_continuous

Picking joint bandwidth of 0.0248
--- finished re-building 'A210-CRM-visualisation.Rmd'

--- re-building 'A220-CRM-pathways.Rmd' using rmarkdown
--- finished re-building 'A220-CRM-pathways.Rmd'

--- re-building 'A250-LevyCaseStudy.Rmd' using rmarkdown
Warning: There were 1990 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: 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ There were 2025 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ Examine the pairs() plot to diagnose sampling problems

Warning: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ There were 2045 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ Examine the pairs() plot to diagnose sampling problems

Warning: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ There were 2013 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ Examine the pairs() plot to diagnose sampling problems

Warning: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ There were 2009 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ Examine the pairs() plot to diagnose sampling problems

Warning: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ There were 2056 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ Examine the pairs() plot to diagnose sampling problems

Warning: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ There were 2006 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ Examine the pairs() plot to diagnose sampling problems

Warning: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map(a0, get_prior_fit)`.
ℹ 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 185 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 66 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 17 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 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: 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: 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: 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: 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map2(a0, beta_inverse_scale, fit_levy_crm, outcomes = "1NNN 3NNT 4NNT 4NNN 4NTN 4TNT")`.
ℹ 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: Problem with `mutate()` column `Mod`.
ℹ `Mod = map2(a0, beta_inverse_scale, fit_levy_crm, outcomes = "1NNN 3NNT 4NNT 4NNN 4NTN 4TNT")`.
ℹ Examine the pairs() plot to diagnose sampling problems

--- finished re-building 'A250-LevyCaseStudy.Rmd'

--- re-building 'A260-TITE-CRM.Rmd' using rmarkdown
--- finished re-building 'A260-TITE-CRM.Rmd'

--- re-building 'A300-NeuenschwanderBransonGsponer.Rmd' using rmarkdown
--- finished re-building 'A300-NeuenschwanderBransonGsponer.Rmd'

--- re-building 'A400-EffTox.Rmd' using rmarkdown
Quitting from lines 235-240 (A400-EffTox.Rmd) 
Error: processing vignette 'A400-EffTox.Rmd' failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building 'A400-EffTox.Rmd'

--- re-building 'A500-HierarchicalBayesianResponse.Rmd' using rmarkdown
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)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file

Attaching package: 'rstan'

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

    extract

ci_level: 0.8 (80% intervals)
outer_level: 0.95 (95% intervals)
--- finished re-building 'A500-HierarchicalBayesianResponse.Rmd'

--- re-building 'A600-BEBOP.Rmd' using rmarkdown
ci_level: 0.8 (80% intervals)
outer_level: 0.95 (95% intervals)
--- finished re-building 'A600-BEBOP.Rmd'

SUMMARY: processing the following file failed:
  'A400-EffTox.Rmd'

Error: Vignette re-building failed.
Execution halted