Running examples in ‘lme4-Ex.R’ failed
The error most likely occurred in:

> ### Name: cbpp
> ### Title: Contagious bovine pleuropneumonia
> ### Aliases: cbpp cbpp2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## response as a matrix
> (m1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
+              family = binomial, data = cbpp))
Generalized linear mixed model fit by maximum likelihood (Laplace
  Approximation) [glmerMod]
 Family: binomial  ( logit )
Formula: cbind(incidence, size - incidence) ~ period + (1 | herd)
   Data: cbpp
      AIC       BIC    logLik -2*log(L)  df.resid 
 194.0531  204.1799  -92.0266  184.0531        51 
Random effects:
 Groups Name        Std.Dev.
 herd   (Intercept) 0.6421  
Number of obs: 56, groups:  herd, 15
Fixed Effects:
(Intercept)      period2      period3      period4  
    -1.3983      -0.9919      -1.1282      -1.5797  
> ## response as a vector of probabilities and usage of argument "weights"
> m1p <- glmer(incidence / size ~ period + (1 | herd), weights = size,
+              family = binomial, data = cbpp)
> ## Confirm that these are equivalent:
> stopifnot(all.equal(fixef(m1), fixef(m1p), tolerance = 1e-5),
+           all.equal(ranef(m1), ranef(m1p), tolerance = 1e-5))
> 
> ## GLMM with individual-level variability (accounting for overdispersion)
> cbpp$obs <- 1:nrow(cbpp)
> (m2 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd) +  (1|obs),
+               family = binomial, data = cbpp))
Generalized linear mixed model fit by maximum likelihood (Laplace
  Approximation) [glmerMod]
 Family: binomial  ( logit )
Formula: cbind(incidence, size - incidence) ~ period + (1 | herd) + (1 |  
    obs)
   Data: cbpp
      AIC       BIC    logLik -2*log(L)  df.resid 
 186.6383  198.7904  -87.3192  174.6383        50 
Random effects:
 Groups Name        Std.Dev.
 obs    (Intercept) 0.8911  
 herd   (Intercept) 0.1840  
Number of obs: 56, groups:  obs, 56; herd, 15
Fixed Effects:
(Intercept)      period2      period3      period4  
     -1.500       -1.226       -1.329       -1.866  
>               
> ## Fitting the model for cbpp2
> gm1 <- glmer(incidence/size ~ period + treatment + avg_size + (1 | herd),
+              family = binomial,
+              data = cbpp2, weights = size,
+              control = glmerControl(optimizer="bobyqa"))
Error: Downdated VtV is not positive definite
Execution halted