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)
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'BEBOP.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed 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

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'CRM-pathways.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- 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


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
`summarise()` ungrouping output (override with `.groups` argument)
--- finished 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

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'CRM.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘CRM.Rmd’

--- re-building ‘EffTox.Rmd’ using rmarkdown
Loading required package: Rcpp
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'EffTox.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed 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)
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'HierarchicalBayesianResponse.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed 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 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: 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 1972 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 2041 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 2059 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 2085 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 2161 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 2101 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

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'LevyCaseStudy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘LevyCaseStudy.Rmd’

--- re-building ‘TITE-CRM.Rmd’ using rmarkdown
Loading required package: Rcpp
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'TITE-CRM.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘TITE-CRM.Rmd’

SUMMARY: processing the following files failed:
  ‘BEBOP.Rmd’ ‘CRM-pathways.Rmd’ ‘CRM.Rmd’ ‘EffTox.Rmd’
  ‘HierarchicalBayesianResponse.Rmd’ ‘LevyCaseStudy.Rmd’ ‘TITE-CRM.Rmd’

Error: Vignette re-building failed.
Execution halted