CRAN Package Check Results for Package HSAUR

Last updated on 2022-01-23 09:58:29 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3-9 2.82 156.56 159.38 OK
r-devel-linux-x86_64-debian-gcc 1.3-9 2.59 132.25 134.84 OK
r-devel-linux-x86_64-fedora-clang 1.3-9 229.84 OK
r-devel-linux-x86_64-fedora-gcc 1.3-9 217.45 OK
r-devel-windows-x86_64-new-UL 1.3-9 100.00 87.00 187.00 OK --no-vignettes
r-devel-windows-x86_64-new-TK 1.3-9 WARN
r-patched-linux-x86_64 1.3-9 3.62 150.91 154.53 OK
r-release-linux-x86_64 1.3-9 3.06 150.71 153.77 OK
r-release-macos-arm64 1.3-9 OK
r-release-macos-x86_64 1.3-9 OK
r-release-windows-ix86+x86_64 1.3-9 8.00 56.00 64.00 OK --no-vignettes
r-oldrel-macos-x86_64 1.3-9 OK
r-oldrel-windows-ix86+x86_64 1.3-9 7.00 40.00 47.00 OK --no-vignettes

Check Details

Version: 1.3-9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'lme4'
Flavor: r-devel-windows-x86_64-new-TK

Version: 1.3-9
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in 'Ch_analysing_longitudinal_dataI.Rnw'
    
    > rm(list = ls())
    
    > s <- search()[-1]
    
    > s <- s[-match(c("package:base", "package:stats", "package:graphics",
    + "package:grDevices", "package:utils", "package:datasets",
    + "packag ..." ... [TRUNCATED]
    
    > if (length(s) > 0) sapply(s, detach, character.only = TRUE)
    
    > if (!file.exists("tables")) dir.create("tables")
    
    > if (!file.exists("figures")) dir.create("figures")
    
    > set.seed(290875)
    
    > options(prompt = "R> ", continue = "+ ", width = 63,
    + SweaveHooks = list(leftpar = function() par(mai = par("mai") *
    + c(1, 1.05, 1, .... [TRUNCATED]
    
    > HSAURpkg <- require("HSAUR")
    Loading required package: HSAUR
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR"))
    
    > rm(HSAURpkg)
    
    > a <- Sys.setlocale("LC_ALL", "C")
    
    > book <- TRUE
    
    > refs <- cbind(c("AItR", "SI", "CI", "ANOVA", "MLR",
    + "GLM", "DE", "RP", "SA", "ALDI", "ALDII", "MA", "PCA", "MDS",
    + "CA"), 1:15)
    
    > ch <- function(x, book = TRUE) {
    + ch <- refs[which(refs[, 1] == x), ]
    + if (book) {
    + return(paste("Chapter~\\\\ref{", ch[1], "}", .... [TRUNCATED]
    
    > library("Matrix")
    
    > library("lme4")
    
     When sourcing 'Ch_analysing_longitudinal_dataI.R':
    Error: there is no package called 'lme4'
    Execution halted
    
     'Ch_analysing_longitudinal_dataI.Rnw' using 'UTF-8'... failed
     'Ch_analysing_longitudinal_dataII.Rnw' using 'UTF-8'... OK
     'Ch_analysis_of_variance.Rnw' using 'UTF-8'... OK
     'Ch_cluster_analysis.Rnw' using 'UTF-8'... OK
     'Ch_conditional_inference.Rnw' using 'UTF-8'... OK
     'Ch_density_estimation.Rnw' using 'UTF-8'... OK
     'Ch_errata.Rnw' using 'UTF-8'... OK
     'Ch_introduction_to_R.Rnw' using 'UTF-8'... OK
     'Ch_logistic_regression_glm.Rnw' using 'UTF-8'... OK
     'Ch_meta_analysis.Rnw' using 'UTF-8'... OK
     'Ch_multidimensional_scaling.Rnw' using 'UTF-8'... OK
     'Ch_multiple_linear_regression.Rnw' using 'UTF-8'... OK
     'Ch_principal_components_analysis.Rnw' using 'UTF-8'... OK
     'Ch_recursive_partitioning.Rnw' using 'UTF-8'... OK
     'Ch_simple_inference.Rnw' using 'UTF-8'... OK
     'Ch_survival_analysis.Rnw' using 'UTF-8'... OK
     'preface.Rnw' using 'UTF-8'... OK
Flavor: r-devel-windows-x86_64-new-TK

Version: 1.3-9
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
    --- re-building 'Ch_analysing_longitudinal_dataI.Rnw' using Sweave
    Loading required package: HSAUR
    Loading required package: tools
    
    Error: processing vignette 'Ch_analysing_longitudinal_dataI.Rnw' failed with diagnostics:
     chunk 2 (label = ALDI-setup)
    Error in library("lme4") : there is no package called 'lme4'
    
    --- failed re-building 'Ch_analysing_longitudinal_dataI.Rnw'
    
    --- re-building 'Ch_analysing_longitudinal_dataII.Rnw' using Sweave
    Loading required package: HSAUR
    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
    --- finished re-building 'Ch_analysing_longitudinal_dataII.Rnw'
    
    --- re-building 'Ch_analysis_of_variance.Rnw' using Sweave
    Loading required package: HSAUR
    Loading required package: tools
    --- finished re-building 'Ch_analysis_of_variance.Rnw'
    
    --- re-building 'Ch_cluster_analysis.Rnw' using Sweave
    Loading required package: HSAUR
    Loading required package: tools
    Package 'mclust' version 5.4.9
    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: HSAUR
    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: HSAUR
    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 5.4.9
    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: HSAUR
    Loading required package: tools
    --- finished re-building 'Ch_errata.Rnw'
    
    --- re-building 'Ch_introduction_to_R.Rnw' using Sweave
    Loading required package: HSAUR
    Loading required package: tools
    --- finished re-building 'Ch_introduction_to_R.Rnw'
    
    --- re-building 'Ch_logistic_regression_glm.Rnw' using Sweave
    Loading required package: HSAUR
    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: HSAUR
    Loading required package: tools
    --- finished re-building 'Ch_meta_analysis.Rnw'
    
    --- re-building 'Ch_multidimensional_scaling.Rnw' using Sweave
    Loading required package: HSAUR
    Loading required package: tools
    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: HSAUR
    Loading required package: tools
    --- finished re-building 'Ch_multiple_linear_regression.Rnw'
    
    --- re-building 'Ch_principal_components_analysis.Rnw' using Sweave
    Loading required package: HSAUR
    Loading required package: tools
    --- finished re-building 'Ch_principal_components_analysis.Rnw'
    
    --- re-building 'Ch_recursive_partitioning.Rnw' using Sweave
    Loading required package: HSAUR
    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
    --- finished re-building 'Ch_recursive_partitioning.Rnw'
    
    --- re-building 'Ch_simple_inference.Rnw' using Sweave
    Loading required package: HSAUR
    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_survival_analysis.Rnw' using Sweave
    Loading required package: HSAUR
    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.bty" is not a graphical parameter
    Warning in plot.window(...) :
     "legend.text" is not a graphical parameter
    Warning in plot.xy(xy, type, ...) :
     "legend.bty" is not a graphical parameter
    Warning in plot.xy(xy, type, ...) :
     "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 axis(side = side, at = at, labels = labels, ...) :
     "legend.text" is not a graphical parameter
    Warning in box(...) : "legend.bty" is not a graphical parameter
    Warning in box(...) : "legend.text" is not a graphical parameter
    Warning in title(...) : "legend.bty" is not a graphical parameter
    Warning in title(...) : "legend.text" is not a graphical parameter
    Warning in approximate(B = 10000) :
     'B' is deprecated; use 'nresample' instead
    --- finished re-building 'Ch_survival_analysis.Rnw'
    
    --- re-building 'preface.Rnw' using Sweave
    --- finished re-building 'preface.Rnw'
    
    SUMMARY: processing the following file failed:
     'Ch_analysing_longitudinal_dataI.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-new-TK