Error(s) in re-building vignettes:
--- re-building 'Ch_analysing_longitudinal_dataI.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

--- finished re-building 'Ch_analysing_longitudinal_dataI.Rnw'

--- re-building 'Ch_analysing_longitudinal_dataII.Rnw' using Sweave
Loading required package: HSAUR2
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
Loading required package: Matrix
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.197453 (tol = 0.002, component 1)
--- finished re-building 'Ch_analysing_longitudinal_dataII.Rnw'

--- re-building 'Ch_analysis_of_variance.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: RColorBrewer
--- finished re-building 'Ch_analysis_of_variance.Rnw'

--- re-building 'Ch_cluster_analysis.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Package 'mclust' version 5.4.7
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: HSAUR2
Loading required package: tools
Loading required package: survival
Warning in chisq.test(suicides) :
  Chi-squared approximation may be incorrect
Warning in approximate(B = 19999) :
  'B' is deprecated; use 'nresample' instead
--- finished re-building 'Ch_conditional_inference.Rnw'

--- re-building 'Ch_density_estimation.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: lattice

Attaching package: 'boot'

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

    boot

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

    melanoma

Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) :
  argument 'replacement' has length > 1 and only the first element will be used
--- finished re-building 'Ch_density_estimation.Rnw'

--- re-building 'Ch_errata.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
--- finished re-building 'Ch_errata.Rnw'

--- re-building 'Ch_gam.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: nlme
This is mgcv 1.8-33. For overview type 'help("mgcv-package")'.
Loading required package: parallel
Loading required package: stabs
Loading required package: RColorBrewer
--- finished re-building 'Ch_gam.Rnw'

--- re-building 'Ch_graphical_display.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
--- finished re-building 'Ch_graphical_display.Rnw'

--- re-building 'Ch_introduction_to_R.Rnw' using Sweave
Loading required package: HSAUR2
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: HSAUR2
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...
--- finished re-building 'Ch_logistic_regression_glm.Rnw'

--- re-building 'Ch_meta_analysis.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
--- finished re-building 'Ch_meta_analysis.Rnw'

--- re-building 'Ch_multidimensional_scaling.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: RColorBrewer
Warning in cmdscale(watervoles, k = 13, eig = TRUE) :
  only 7 of the first 13 eigenvalues are > 0
--- finished re-building 'Ch_multidimensional_scaling.Rnw'

--- re-building 'Ch_multiple_linear_regression.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: RColorBrewer
--- finished re-building 'Ch_multiple_linear_regression.Rnw'

--- re-building 'Ch_principal_components_analysis.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
--- finished re-building 'Ch_principal_components_analysis.Rnw'

--- re-building 'Ch_recursive_partitioning.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: grid
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: libcoin

Attaching package: 'partykit'

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

    cforest, ctree, ctree_control, edge_simple, mob,
    mob_control, node_barplot, node_bivplot,
    node_boxplot, node_inner, node_surv, node_terminal,
    varimp

--- finished re-building 'Ch_recursive_partitioning.Rnw'

--- re-building 'Ch_simple_inference.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: grid
Warning in wilcox.test.default(mooringdiff) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(mooringdiff) :
  cannot compute exact p-value with ties
--- finished re-building 'Ch_simple_inference.Rnw'

--- re-building 'Ch_simultaneous_inference.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Loading required package: Matrix
--- finished re-building 'Ch_simultaneous_inference.Rnw'

--- re-building 'Ch_survival_analysis.Rnw' using Sweave
Loading required package: HSAUR2
Loading required package: tools
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Warning in plot.window(...) :
  "legend.text" is not a graphical parameter
Warning in plot.window(...) : "legend.bty" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "legend.text" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "legend.bty" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "legend.text" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "legend.bty" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "legend.text" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "legend.bty" is not a graphical parameter
Warning in box(...) : "legend.text" is not a graphical parameter
Warning in box(...) : "legend.bty" is not a graphical parameter
Warning in title(...) : "legend.text" is not a graphical parameter
Warning in title(...) : "legend.bty" is not a graphical parameter
Warning in approximate(B = 10000) :
  'B' is deprecated; use 'nresample' instead
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "Ch_survival_analysis.tex" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'Ch_survival_analysis.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'Ch_survival_analysis.pdf' for vignette with name 'Ch_survival_analysis' and engine 'utils::Sweave'. 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--- failed re-building 'Ch_survival_analysis.Rnw'

SUMMARY: processing the following file failed:
  'Ch_survival_analysis.Rnw'

Error: Vignette re-building failed.
Execution halted