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--- re-building ‘Ch_analysing_longitudinal_dataI.Rnw’ using Sweave
Loading required package: HSAUR3
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Attaching package: 'TH.data'

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

--- re-building 'Ch_analysing_longitudinal_dataII.Rnw' using Sweave
Loading required package: HSAUR3
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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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running glm to get initial regression estimate
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
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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,  :
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--- finished re-building 'Ch_analysing_longitudinal_dataII.Rnw'

--- re-building 'Ch_analysis_of_variance.Rnw' using Sweave
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--- re-building 'Ch_bayesian_inference.Rnw' using Sweave
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--- finished 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 6.0.0
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'mvtnorm'

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Error: processing vignette 'Ch_cluster_analysis.Rnw' failed with diagnostics:
 chunk 5 (label = CA-pottery-distplot) 
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--- failed re-building 'Ch_cluster_analysis.Rnw'

--- re-building 'Ch_conditional_inference.Rnw' using Sweave
Loading required package: HSAUR3
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Warning in chisq.test(suicides) :
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--- finished re-building 'Ch_conditional_inference.Rnw'

--- re-building 'Ch_density_estimation.Rnw' using Sweave
Loading required package: HSAUR3
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KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
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Package 'mclust' version 6.0.0
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--- re-building 'Ch_graphical_display.Rnw' using Sweave
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Loading required package: HSAUR3
Loading required package: tools
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Error: processing vignette 'Ch_quantile_regression.Rnw' failed with diagnostics:
polygon edge not found
--- failed re-building 'Ch_quantile_regression.Rnw'

--- re-building 'Ch_recursive_partitioning.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
Loading required package: grid
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.
Loading required package: libcoin
Loading required package: mvtnorm
Warning in length(just) : closing unused connection 4 ()
--- finished re-building 'Ch_recursive_partitioning.Rnw'

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

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

    birds

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

--- re-building 'Ch_survival_analysis.Rnw' using Sweave
Loading required package: HSAUR3
Loading required package: tools
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
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
--- finished re-building 'Ch_survival_analysis.Rnw'

SUMMARY: processing the following files failed:
  'Ch_cluster_analysis.Rnw' 'Ch_graphical_display.Rnw'
  'Ch_quantile_regression.Rnw'

Error: Vignette re-building failed.
Execution halted