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

Error: processing vignette 'Ch_analysing_longitudinal_dataII.Rnw' failed with diagnostics:
 chunk 4 (label = ALDII-gee) 
Error in library("gee") : there is no package called 'gee'

--- 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

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

--- failed 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 1.8-39. 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("sp") : there is no package called 'sp'

--- 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: processing vignette 'Ch_introduction_to_R.Rnw' failed with diagnostics:
 chunk 42 (label = AItR-Forbes2000-files) 
Error in setwd(filep) : cannot change working directory

--- failed 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

Error: processing vignette 'Ch_meta_analysis.Rnw' failed with diagnostics:
 chunk 4 (label = MA-smoking-OR) 
Error in library("rmeta") : there is no package called 'rmeta'

--- failed re-building 'Ch_meta_analysis.Rnw'

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

Error: processing vignette 'Ch_missing_values.Rnw' failed with diagnostics:
 chunk 10 (label = MV-bp-mice-pkg) 
Error in library("mice") : there is no package called 'mice'

--- failed 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("ape") : there is no package called 'ape'

--- 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
Warning in trellis.par.set(list(plot.symbol = list(col = 1, pch = 20, cex = 0.7),  :
  Note: The default device has been opened to honour attempt to modify trellis settings

Error: processing vignette 'Ch_quantile_regression.Rnw' failed with diagnostics:
 chunk 3 (label = QR-setup) 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'gamlss.data'

--- 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_cluster_analysis.Rnw'
  'Ch_conditional_inference.Rnw'
  'Ch_density_estimation.Rnw' 'Ch_gam.Rnw'
  'Ch_graphical_display.Rnw' 'Ch_introduction_to_R.Rnw'
  'Ch_logistic_regression_glm.Rnw'
  'Ch_meta_analysis.Rnw' 'Ch_missing_values.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