CRAN Package Check Results for Package HSAUR3

Last updated on 2020-02-20 15:48:28 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0-9 4.27 217.69 221.96 WARN
r-devel-linux-x86_64-debian-gcc 1.0-9 3.25 172.35 175.60 OK
r-devel-linux-x86_64-fedora-clang 1.0-9 294.95 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0-9 286.43 OK
r-devel-windows-ix86+x86_64 1.0-9 11.00 83.00 94.00 OK --no-vignettes
r-devel-windows-ix86+x86_64-gcc8 1.0-9 17.00 66.00 83.00 OK --no-vignettes
r-patched-linux-x86_64 1.0-9 3.28 205.39 208.67 OK
r-patched-solaris-x86 1.0-9 400.20 NOTE
r-release-linux-x86_64 1.0-9 3.66 205.22 208.88 OK
r-release-windows-ix86+x86_64 1.0-9 11.00 69.00 80.00 OK --no-vignettes
r-release-osx-x86_64 1.0-9 OK
r-oldrel-windows-ix86+x86_64 1.0-9 8.00 51.00 59.00 OK --no-vignettes
r-oldrel-osx-x86_64 1.0-9 OK

Check Details

Version: 1.0-9
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: HSAUR3
    Loading required package: tools
    Loading required package: Matrix
    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
    
    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: HSAUR3
    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: HSAUR3
    Loading required package: tools
    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: tools
    Loading required package: survival
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    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_bayesian_inference.Rnw'
    
    --- re-building 'Ch_cluster_analysis.Rnw' using Sweave
    Loading required package: HSAUR3
    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: HSAUR3
    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: HSAUR3
    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: HSAUR3
    Loading required package: tools
    --- finished re-building 'Ch_errata.Rnw'
    
    --- re-building 'Ch_gam.Rnw' using Sweave
    Loading required package: HSAUR3
    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: HSAUR3
    Loading required package: tools
    Checking rgeos availability: TRUE
    --- finished re-building 'Ch_graphical_display.Rnw'
    
    --- re-building 'Ch_introduction_to_R.Rnw' using Sweave
    Loading required package: HSAUR3
    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: HSAUR3
    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...
    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
    Loading required package: tools
    --- finished re-building 'Ch_meta_analysis.Rnw'
    
    --- re-building 'Ch_missing_values.Rnw' using Sweave
    Loading required package: HSAUR3
    Loading required package: tools
    Loading required package: lattice
    
    Attaching package: 'mice'
    
    The following object is masked from 'package:HSAUR3':
    
     toenail
    
    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: 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: HSAUR3
    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: HSAUR3
    Loading required package: tools
    --- finished re-building 'Ch_principal_components_analysis.Rnw'
    
    --- re-building 'Ch_quantile_regression.Rnw' using Sweave
    Loading required package: HSAUR3
    Loading required package: tools
    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
    
    Attaching package: 'SparseM'
    
    The following object is masked from 'package:base':
    
     backsolve
    
    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: tools
    Loading required package: grid
    randomForest 4.6-14
    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: 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 file failed:
     'Ch_conditional_inference.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0-9
Check: installed package size
Result: NOTE
     installed size is 5.0Mb
     sub-directories of 1Mb or more:
     doc 3.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86