Error(s) in re-building vignettes:
  ...
--- re-building ‘compareGroups_vignette.Rmd’ using rmarkdown
Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: SNPassoc
Loading required package: haplo.stats
Loading required package: survival
Loading required package: mvtnorm
Loading required package: parallel
Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-14'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-15'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-23'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-24'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-30'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor.test.default(x, as.integer(y), method = "spearman") :
  Cannot compute exact p-value with ties
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-31'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
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Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-35'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-36'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-70'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-72'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-74'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-76'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-77'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-79'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-83'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-84'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-85'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-86'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-87'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-88'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-89'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-90'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-91'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-92'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-93'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-95'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
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Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-97'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in cor(as.integer(x), as.integer(y)) :
  the standard deviation is zero
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-98'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-99'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-100'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-101'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-102'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-103'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-104'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-105'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-109'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'compareGroups_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘compareGroups_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted