Error(s) in re-building vignettes:
--- re-building ‘compareGroups_vignette.Rmd’ using rmarkdown
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Loading required package: SNPassoc
Loading required package: haplo.stats
Loading required package: survival
Loading required package: mvtnorm
Loading required package: parallel
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  variable 'age7gr' converted to factor since few different values contained
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in norm.plot(x = x.var, file = file.i, var.label.x = var.labels[i],  :
  p-value for normality in Age could not be calculated
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compareGroups.fit(X = X, y = y, include.label = include.label,  :
  variables tovent specified in 'method' not found
Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in chisq.test(xx, correct = FALSE) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(xx, correct = FALSE) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(xx, correct = FALSE) :
  Chi-squared approximation may be incorrect
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'smk' are removed since no observation in that/those levels
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'sex' are removed since no observation in that/those levels
Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'smk' are removed since no observation in that/those levels
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'smk' are removed since no observation in that/those levels
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'smk' are removed since no observation in that/those levels
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'smk' are removed since no observation in that/those levels
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'year' are removed since no observation in that/those levels
Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i],  :
  Some levels of 'sex' are removed since no observation in that/those levels
Warning in fitter(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  3 ; coefficient may be infinite. 
Warning in fitter(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  2 ; coefficient may be infinite. 
Warning in fitter(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  2 ; coefficient may be infinite. 
Warning in fitter(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  2 ; coefficient may be infinite. 
Warning in fitter(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  2 ; coefficient may be infinite. 
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in HWChisq(X[i, ], ...) :
  Expected counts below 5: chi-square approximation may be incorrect
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in HWChisq(X[i, ], ...) :
  Expected counts below 5: chi-square approximation may be incorrect
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in HWChisq(X[i, ], ...) :
  Expected counts below 5: chi-square approximation may be incorrect
Warning in HWf(X) : Monomorphic marker, f set to zero.
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in HWChisq(X[i, ], ...) :
  Expected counts below 5: chi-square approximation may be incorrect
Warning in HWf(X) : Monomorphic marker, f set to zero.
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in homozyg(X) :
  Genotypes are not labelled, default labels (AA, AB, BB) assumed.
Warning in heterozyg(X) :
  Genotypes are not labelled, default labels assumed.
Warning in HWChisq(X[i, ], ...) :
  Expected counts below 5: chi-square approximation may be incorrect
Warning in HWf(X) : Monomorphic marker, f set to zero.
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
Warning in base::deparse(e, width) :
  invalid 'cutoff' value for 'deparse', using default
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'compareGroups_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘compareGroups_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘compareGroups_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted