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--- re-building ‘Ch_analysing_longitudinal_dataI.Rnw’ using Sweave
Loading required package: HSAUR
Loading required package: tools
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00253824 (tol = 0.002, component 1)
Error: processing vignette 'Ch_analysing_longitudinal_dataI.Rnw' failed with diagnostics:
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--- failed re-building 'Ch_analysing_longitudinal_dataI.Rnw'

--- re-building ‘Ch_analysing_longitudinal_dataII.Rnw’ using Sweave
Loading required package: HSAUR
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Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
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Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
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Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
Error: processing vignette 'Ch_analysing_longitudinal_dataII.Rnw' failed with diagnostics:
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--- failed re-building 'Ch_analysing_longitudinal_dataII.Rnw'

--- re-building ‘Ch_analysis_of_variance.Rnw’ using Sweave
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--- failed re-building 'Ch_analysis_of_variance.Rnw'

--- re-building ‘Ch_cluster_analysis.Rnw’ using Sweave
Loading required package: HSAUR
Loading required package: tools
Package 'mclust' version 5.4.5
Type 'citation("mclust")' for citing this R package in publications.

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--- failed re-building 'Ch_cluster_analysis.Rnw'

--- re-building ‘Ch_conditional_inference.Rnw’ using Sweave
Loading required package: HSAUR
Loading required package: tools
Loading required package: survival
Warning in chisq.test(suicides) :
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Warning in approximate(B = 19999) :
  'B' is deprecated; use 'nresample' instead
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--- failed re-building 'Ch_conditional_inference.Rnw'

--- re-building ‘Ch_density_estimation.Rnw’ using Sweave
Loading required package: HSAUR
Loading required package: tools
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: lattice

Attaching package: 'boot'

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Type 'citation("mclust")' for citing this R package in publications.
Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) :
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--- failed re-building 'Ch_density_estimation.Rnw'

--- re-building ‘Ch_errata.Rnw’ using Sweave
Loading required package: HSAUR
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--- finished re-building 'Ch_errata.Rnw'

--- re-building ‘Ch_introduction_to_R.Rnw’ using Sweave
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--- re-building ‘Ch_logistic_regression_glm.Rnw’ using Sweave
Loading required package: HSAUR
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'Ch_principal_components_analysis.Rnw'

--- re-building ‘Ch_recursive_partitioning.Rnw’ using Sweave
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randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
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Error: processing vignette 'Ch_recursive_partitioning.Rnw' failed with diagnostics:
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'Ch_recursive_partitioning.Rnw'

--- re-building ‘Ch_simple_inference.Rnw’ using Sweave
Loading required package: HSAUR
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Warning in wilcox.test.default(mooringdiff) :
  cannot compute exact p-value with ties
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  cannot compute exact p-value with ties
Error: processing vignette 'Ch_simple_inference.Rnw' failed with diagnostics:
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'Ch_simple_inference.Rnw'

--- re-building ‘Ch_survival_analysis.Rnw’ using Sweave
Loading required package: HSAUR
Loading required package: tools
Loading required package: grid
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Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

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Loading required package: sandwich
Warning in plot.window(...) : "legend.bty" is not a graphical parameter
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Warning in plot.xy(xy, type, ...) :
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Error: processing vignette 'Ch_survival_analysis.Rnw' failed with diagnostics:
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'Ch_survival_analysis.Rnw'

--- re-building ‘preface.Rnw’ using Sweave
Loading required package: HSAUR
Loading required package: tools
--- finished re-building 'preface.Rnw'

SUMMARY: processing the following files failed:
  ‘Ch_analysing_longitudinal_dataI.Rnw’
  ‘Ch_analysing_longitudinal_dataII.Rnw’ ‘Ch_analysis_of_variance.Rnw’
  ‘Ch_cluster_analysis.Rnw’ ‘Ch_conditional_inference.Rnw’
  ‘Ch_density_estimation.Rnw’ ‘Ch_introduction_to_R.Rnw’
  ‘Ch_logistic_regression_glm.Rnw’ ‘Ch_meta_analysis.Rnw’
  ‘Ch_multidimensional_scaling.Rnw’ ‘Ch_multiple_linear_regression.Rnw’
  ‘Ch_principal_components_analysis.Rnw’
  ‘Ch_recursive_partitioning.Rnw’ ‘Ch_simple_inference.Rnw’
  ‘Ch_survival_analysis.Rnw’

Error: Vignette re-building failed.
Execution halted