Error(s) in re-building vignettes:
  ...
--- re-building ‘Ch_analysing_longitudinal_dataI.Rnw’ using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_analysing_longitudinal_dataI.Rnw' failed with diagnostics:
 chunk 3 (label = ALDI-setup) 
Error in library("lme4") : there is no package called 'lme4'

--- failed re-building 'Ch_analysing_longitudinal_dataI.Rnw'

--- re-building 'Ch_analysing_longitudinal_dataII.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
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
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:
 chunk 26 (label = ALDII-respiratory-lmer) 
Error in library("lme4") : there is no package called 'lme4'

--- failed re-building 'Ch_analysing_longitudinal_dataII.Rnw'

--- re-building 'Ch_analysis_of_variance.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_analysis_of_variance.Rnw' failed with diagnostics:
 chunk 3 (label = ANOVA-setup) 
Error in library("wordcloud") : there is no package called 'wordcloud'

--- failed re-building 'Ch_analysis_of_variance.Rnw'

--- re-building 'Ch_bayesian_inference.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_bayesian_inference.Rnw' failed with diagnostics:
 chunk 7 (label = BI-M-it) 
Error in library("coin") : there is no package called 'coin'

--- failed re-building 'Ch_bayesian_inference.Rnw'

--- re-building 'Ch_cluster_analysis.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
Package 'mclust' version 5.4.9
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'mvtnorm'

The following object is masked from 'package:mclust':

    dmvnorm

--- finished re-building 'Ch_cluster_analysis.Rnw'

--- re-building 'Ch_conditional_inference.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_conditional_inference.Rnw' failed with diagnostics:
 chunk 3 (label = CI-roomwidth-ties) 
Error in library("coin") : there is no package called 'coin'

--- failed re-building 'Ch_conditional_inference.Rnw'

--- re-building 'Ch_density_estimation.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Error: processing vignette 'Ch_density_estimation.Rnw' failed with diagnostics:
 chunk 3 (label = DE-setup) 
Error in library("flexmix") : there is no package called 'flexmix'

--- failed re-building 'Ch_density_estimation.Rnw'

--- re-building 'Ch_errata.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
--- finished re-building 'Ch_errata.Rnw'

--- re-building 'Ch_gam.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.

Error: processing vignette 'Ch_gam.Rnw' failed with diagnostics:
 chunk 3 (label = packages) 
Error in library("mboost") : there is no package called 'mboost'

--- failed re-building 'Ch_gam.Rnw'

--- re-building 'Ch_graphical_display.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_graphical_display.Rnw' failed with diagnostics:
 chunk 10 (label = DAGD-USmelanoma-long-lat-data) 
Error in library("maptools") : there is no package called 'maptools'

--- failed re-building 'Ch_graphical_display.Rnw'

--- re-building 'Ch_introduction_to_R.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
Error in quantile.default(x, prob = c(0.25, 0.75), names = FALSE) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE
--- finished re-building 'Ch_introduction_to_R.Rnw'

--- re-building 'Ch_logistic_regression_glm.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...

Error: processing vignette 'Ch_logistic_regression_glm.Rnw' failed with diagnostics:
 chunk 36 (label = GLM-CHFLS-polr-cftest) 
Error in library("multcomp") : there is no package called 'multcomp'

--- failed re-building 'Ch_logistic_regression_glm.Rnw'

--- re-building 'Ch_meta_analysis.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
--- finished re-building 'Ch_meta_analysis.Rnw'

--- re-building 'Ch_missing_values.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Attaching package: 'mice'

The following object is masked from 'package:HSAUR3':

    toenail

The following object is masked from 'package:stats':

    filter

The following objects are masked from 'package:base':

    cbind, rbind

--- finished re-building 'Ch_missing_values.Rnw'

--- re-building 'Ch_multidimensional_scaling.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_multidimensional_scaling.Rnw' failed with diagnostics:
 chunk 3 (label = MDS-setup) 
Error in library("wordcloud") : there is no package called 'wordcloud'

--- failed re-building 'Ch_multidimensional_scaling.Rnw'

--- re-building 'Ch_multiple_linear_regression.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_multiple_linear_regression.Rnw' failed with diagnostics:
 chunk 3 (label = MLR-setup) 
Error in library("wordcloud") : there is no package called 'wordcloud'

--- failed re-building 'Ch_multiple_linear_regression.Rnw'

--- re-building 'Ch_principal_components_analysis.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
--- finished re-building 'Ch_principal_components_analysis.Rnw'

--- re-building 'Ch_quantile_regression.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_quantile_regression.Rnw' failed with diagnostics:
 chunk 8 (label = QR-db-median) 
Error in library("quantreg") : there is no package called 'quantreg'

--- failed re-building 'Ch_quantile_regression.Rnw'

--- re-building 'Ch_recursive_partitioning.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_recursive_partitioning.Rnw' failed with diagnostics:
 chunk 3 (label = RP-setup) 
Error in library("vcd") : there is no package called 'vcd'

--- failed re-building 'Ch_recursive_partitioning.Rnw'

--- re-building 'Ch_simple_inference.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_simple_inference.Rnw' failed with diagnostics:
 chunk 3 (label = SI-setup) 
Error in library("vcd") : there is no package called 'vcd'

--- failed re-building 'Ch_simple_inference.Rnw'

--- re-building 'Ch_simultaneous_inference.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_simultaneous_inference.Rnw' failed with diagnostics:
 chunk 3 (label = SIMC-setup) 
Error in library("multcomp") : there is no package called 'multcomp'

--- failed re-building 'Ch_simultaneous_inference.Rnw'

--- re-building 'Ch_survival_analysis.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools

Error: processing vignette 'Ch_survival_analysis.Rnw' failed with diagnostics:
 chunk 3 (label = SA-setup) 
Error in library("coin") : there is no package called 'coin'

--- failed re-building 'Ch_survival_analysis.Rnw'

SUMMARY: processing the following files failed:
  'Ch_analysing_longitudinal_dataI.Rnw'
  'Ch_analysing_longitudinal_dataII.Rnw'
  'Ch_analysis_of_variance.Rnw'
  'Ch_bayesian_inference.Rnw'
  'Ch_conditional_inference.Rnw'
  'Ch_density_estimation.Rnw' 'Ch_gam.Rnw'
  'Ch_graphical_display.Rnw'
  'Ch_logistic_regression_glm.Rnw'
  'Ch_multidimensional_scaling.Rnw'
  'Ch_multiple_linear_regression.Rnw'
  'Ch_quantile_regression.Rnw'
  'Ch_recursive_partitioning.Rnw'
  'Ch_simple_inference.Rnw'
  'Ch_simultaneous_inference.Rnw'
  'Ch_survival_analysis.Rnw'

Error: Vignette re-building failed.
Execution halted