Error(s) in re-building vignettes:
--- re-building ‘x1_introAndDataPrepVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘x1_introAndDataPrepVignette.Rmd’

--- re-building ‘x2_rawDataProcessingVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘x2_rawDataProcessingVignette.Rmd’

--- re-building ‘x3_hyperParameterVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in dnbinom(ni, size = size_f2, prob = prob_f2) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in pnbinom(sum_limit, size = size_f2, prob = prob_f2) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in dnbinom(ni, size = size_f2, prob = prob_f2) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in pnbinom(sum_limit, size = size_f2, prob = prob_f2) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in dnbinom(ni, size = size_f2, prob = prob_f2) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in pnbinom(sum_limit, size = size_f2, prob = prob_f2) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in stats::nlm(negLLsquash, p = theta_init, ni = squashed$N, ei = squashed$E,  :
  NA/Inf replaced by maximum positive value
Warning in dnbinom(N, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLL,  :
  NA/NaN function evaluation
Warning in dnbinom(N, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLL,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 279-290 (x3_hyperParameterVignette.Rmd) 
Error: processing vignette 'x3_hyperParameterVignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘x3_hyperParameterVignette.Rmd’

--- re-building ‘x4_posteriorCalculationVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f2, prob = prob_f2) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f2, prob = prob_f2) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
--- finished re-building ‘x4_posteriorCalculationVignette.Rmd’

--- re-building ‘x5_openEBGMObjectVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f1, prob = prob_f1) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f1, prob = prob_f1) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in dnbinom(ni, size = size_f2, prob = prob_f2) : NaNs produced
Warning in pnbinom(sum_limit, size = size_f2, prob = prob_f2) :
  NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced
Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash,  :
  NA/NaN function evaluation
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Quitting from lines 97-98 (x5_openEBGMObjectVignette.Rmd) 
Error: processing vignette 'x5_openEBGMObjectVignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘x5_openEBGMObjectVignette.Rmd’

SUMMARY: processing the following files failed:
  ‘x3_hyperParameterVignette.Rmd’ ‘x5_openEBGMObjectVignette.Rmd’

Error: Vignette re-building failed.
Execution halted