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

Attaching package: 'lme4'

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

    schizophrenia

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

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

--- re-building ‘Ch_analysing_longitudinal_dataII.Rnw’ using Sweave
Loading required package: HSAUR3
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

Attaching package: 'lme4'

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

    schizophrenia


Error: processing vignette 'Ch_analysing_longitudinal_dataII.Rnw' failed with diagnostics:
 chunk 26 (label = ALDII-respiratory-lmer) 
Error in eval(expr, .GlobalEnv) : Downdated VtV is not positive definite

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

--- re-building ‘Ch_analysis_of_variance.Rnw’ using Sweave
Loading required package: HSAUR3
Loading required package: RColorBrewer
--- finished re-building 'Ch_analysis_of_variance.Rnw'

--- re-building ‘Ch_bayesian_inference.Rnw’ using Sweave
Loading required package: HSAUR3
Loading required package: survival
Waiting for profiling to be done...
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--- finished re-building 'Ch_bayesian_inference.Rnw'

--- re-building ‘Ch_cluster_analysis.Rnw’ using Sweave
Loading required package: HSAUR3
Package 'mclust' version 6.1.3
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: survival
Warning in chisq.test(suicides) :
  Chi-squared approximation may be incorrect
--- finished re-building 'Ch_conditional_inference.Rnw'

--- re-building ‘Ch_density_estimation.Rnw’ using Sweave
Loading required package: HSAUR3
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 6.1.3
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: HSAUR3
--- finished re-building 'Ch_errata.Rnw'

--- re-building ‘Ch_gam.Rnw’ using Sweave
Loading required package: HSAUR3
Loading required package: nlme
This is mgcv 1.9-4. For overview type '?mgcv'.
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: HSAUR3
Linking to GEOS 3.14.1, GDAL 3.13.1, PROJ 9.8.1; sf_use_s2()
is TRUE
--- finished re-building 'Ch_graphical_display.Rnw'

--- re-building ‘Ch_introduction_to_R.Rnw’ using Sweave
Loading required package: HSAUR3
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
Waiting for profiling to be done...
Waiting for profiling to be done...
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Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

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

    geyser

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

    birds

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: HSAUR3
--- finished re-building 'Ch_meta_analysis.Rnw'

--- re-building ‘Ch_missing_values.Rnw’ using Sweave
Loading required package: HSAUR3

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: 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: HSAUR3
Loading required package: RColorBrewer
--- finished re-building 'Ch_multiple_linear_regression.Rnw'

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

--- re-building ‘Ch_quantile_regression.Rnw’ using Sweave
Loading required package: HSAUR3
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
Loading required package: SparseM
Warning in rq.fit.br(x, y, tau = tau, ci = TRUE, ...) :
  Solution may be nonunique
Warning in rq.fit.br(x, y, tau = tau, ci = TRUE, ...) :
  Solution may be nonunique
--- finished re-building 'Ch_quantile_regression.Rnw'

--- re-building ‘Ch_recursive_partitioning.Rnw’ using Sweave
Loading required package: HSAUR3
Loading required package: grid
randomForest 4.7-1.2
Type rfNews() to see new features/changes/bug fixes.
Loading required package: libcoin
Loading required package: mvtnorm
--- finished re-building 'Ch_recursive_partitioning.Rnw'

--- re-building ‘Ch_simple_inference.Rnw’ using Sweave
Loading required package: HSAUR3
Loading required package: grid
--- finished re-building 'Ch_simple_inference.Rnw'

--- re-building ‘Ch_simultaneous_inference.Rnw’ using Sweave
Loading required package: HSAUR3
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

Attaching package: 'lme4'

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

    schizophrenia

--- finished re-building 'Ch_simultaneous_inference.Rnw'

--- re-building ‘Ch_survival_analysis.Rnw’ using Sweave
Loading required package: HSAUR3
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
--- finished re-building 'Ch_survival_analysis.Rnw'

SUMMARY: processing the following file failed:
  ‘Ch_analysing_longitudinal_dataII.Rnw’

Error: Vignette re-building failed.
Execution halted