Error(s) in re-building vignettes:
  ...
--- re-building ‘eHOF.Rnw’ using knitr
Some columns contain no data and are omitted.
Some numeric columns contain only 0 values and are omitted.
Some numeric fields contain 0 values:
Please check if these are really meant as 0 or if they are erroneously assigned because of DBase restrictions.
If so, use something like:
site$Column_name[site$Column_name==0] <- NA

Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in dbinom(round(m * y), round(m), mu, log = TRUE) :
  NaNs produced
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in nlminb(start = p, objective = mlHOF, lower = -lim, upper = lim,  :
  NA/NaN function evaluation
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Warning in par()$mar + c(0, 0, 2) :
  longer object length is not a multiple of shorter object length
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges (‘box’): maybe set notch=FALSE
Error: processing vignette ‘eHOF.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘eHOF.tex’ failed.
LaTeX errors:
! You can't use `macro parameter character #' in horizontal mode.
l.85 library(eHOF)#
                   # Loading required package: mgcv
? 
! Emergency stop.
! Emergency stop.
l.85 library(eHOF)#
                   # Loading required package: mgcv
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘eHOF.Rnw’

SUMMARY: processing the following file failed:
  ‘eHOF.Rnw’

Error: Vignette re-building failed.
Execution halted