• using R version 4.6.1 Patched (2026-06-28 r90209)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.3.0-1) 15.3.0     GNU Fortran (Debian 15.3.0-1) 15.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-08 04:52:48 UTC
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• this is package ‘HSAUR2’ version ‘1.1-21’
• package encoding: UTF-8
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[109s/158s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Ch_analysing_longitudinal_dataI.Rnw’ using Sweave Loading required package: HSAUR2 Loading required package: tools Attaching package: 'lme4' The following object is masked from 'package:HSAUR2':     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 --- 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 Attaching package: 'lme4' The following object is masked from 'package:HSAUR2':     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: 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 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: 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 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: 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 1.9-4. 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: 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 4.7-1.2 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 --- 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 Attaching package: 'lme4' The following object is masked from 'package:HSAUR2':     schizophrenia Error: processing vignette 'Ch_simultaneous_inference.Rnw' failed with diagnostics:  chunk 12 (label = SIMC-trees-lmer) Error in eval(expr, .GlobalEnv) : Downdated VtV is not positive definite --- failed 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 --- finished re-building 'Ch_survival_analysis.Rnw' SUMMARY: processing the following files failed:   ‘Ch_analysing_longitudinal_dataII.Rnw’   ‘Ch_simultaneous_inference.Rnw’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [4s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR