Error(s) in re-building vignettes:
  ...
--- re-building 'x1_introAndDataPrepVignette.Rmd' using rmarkdown
Quitting from lines 173-176 (x1_introAndDataPrepVignette.Rmd) 
Error: processing vignette 'x1_introAndDataPrepVignette.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'x1_introAndDataPrepVignette.Rmd'

--- re-building 'x2_rawDataProcessingVignette.Rmd' using rmarkdown
--- finished re-building 'x2_rawDataProcessingVignette.Rmd'

--- re-building 'x3_hyperParameterVignette.Rmd' using rmarkdown
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 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_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
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 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
Quitting from lines 279-290 (x3_hyperParameterVignette.Rmd) 
Error: processing vignette 'x3_hyperParameterVignette.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'x3_hyperParameterVignette.Rmd'

--- re-building 'x4_posteriorCalculationVignette.Rmd' using rmarkdown
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 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
--- finished re-building 'x5_openEBGMObjectVignette.Rmd'

SUMMARY: processing the following files failed:
  'x1_introAndDataPrepVignette.Rmd' 'x3_hyperParameterVignette.Rmd'

Error: Vignette re-building failed.
Execution halted