CRAN Package Check Results for Package HSAUR2

Last updated on 2020-02-19 11:49:13 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-17 3.87 176.78 180.65 WARN
r-devel-linux-x86_64-debian-gcc 1.1-17 3.23 138.73 141.96 WARN
r-devel-linux-x86_64-fedora-clang 1.1-17 243.07 OK
r-devel-linux-x86_64-fedora-gcc 1.1-17 237.30 OK
r-devel-windows-ix86+x86_64 1.1-17 11.00 291.00 302.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.1-17 13.00 427.00 440.00 OK
r-patched-linux-x86_64 1.1-17 2.86 167.55 170.41 OK
r-patched-solaris-x86 1.1-17 312.00 OK
r-release-linux-x86_64 1.1-17 2.86 169.12 171.98 OK
r-release-windows-ix86+x86_64 1.1-17 8.00 287.00 295.00 OK
r-release-osx-x86_64 1.1-17 OK
r-oldrel-windows-ix86+x86_64 1.1-17 7.00 262.00 269.00 OK
r-oldrel-osx-x86_64 1.1-17 OK

Check Details

Version: 1.1-17
Check: re-building of vignette outputs
Result: WARN
    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
    
    Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
     Model failed to converge with max|grad| = 0.00299323 (tol = 0.002, component 1)
    --- 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| = 0.197379 (tol = 0.001, 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 5.4.5
    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
    
    Error: processing vignette 'Ch_conditional_inference.Rnw' failed with diagnostics:
     chunk 22 (label = CI-anomalies-mh)
    Error in NROW(x) : argument "x" is missing, with no default
    
    --- failed 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 5.4.5
    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 1.8-31. For overview type 'help("mgcv-package")'.
    Loading required package: parallel
    Loading required package: stabs
    This is mboost 2.9-2. See 'package?mboost' and 'news(package = "mboost")'
    for a complete list of changes.
    
    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
    Warning in if (class(X) == "dist") X <- as.matrix(X) :
     the condition has length > 1 and only the first element will be used
    --- 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
    --- finished re-building 'Ch_survival_analysis.Rnw'
    
    SUMMARY: processing the following file failed:
     'Ch_conditional_inference.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1-17
Check: re-building of vignette outputs
Result: WARN
    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
    
    Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
     Model failed to converge with max|grad| = 0.00299323 (tol = 0.002, component 1)
    --- 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| = 0.19738 (tol = 0.001, 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 5.4.5
    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
    
    Error: processing vignette 'Ch_conditional_inference.Rnw' failed with diagnostics:
     chunk 22 (label = CI-anomalies-mh)
    Error in NROW(x) : argument "x" is missing, with no default
    
    --- failed 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 5.4.5
    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 1.8-31. For overview type 'help("mgcv-package")'.
    Loading required package: parallel
    Loading required package: stabs
    This is mboost 2.9-2. See 'package?mboost' and 'news(package = "mboost")'
    for a complete list of changes.
    
    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
    Warning in if (class(X) == "dist") X <- as.matrix(X) :
     the condition has length > 1 and only the first element will be used
    --- 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
    --- finished re-building 'Ch_survival_analysis.Rnw'
    
    SUMMARY: processing the following file failed:
     ‘Ch_conditional_inference.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc