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
when running code in 'Ch_analysing_longitudinal_dataII.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("gee")

  When sourcing 'Ch_analysing_longitudinal_dataII.R':
Error: there is no package called 'gee'
Execution halted
when running code in 'Ch_cluster_analysis.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("mclust")

  When sourcing 'Ch_cluster_analysis.R':
Error: there is no package called 'mclust'
Execution halted
when running code in 'Ch_conditional_inference.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] 

> data("roomwidth", package = "HSAUR")

> nobs <- table(roomwidth$unit)

> ties <- tapply(roomwidth$width, roomwidth$unit, function(x) length(x) - 
+     length(unique(x)))

> library("coin")

  When sourcing 'Ch_conditional_inference.R':
Error: there is no package called 'coin'
Execution halted
when running code in 'Ch_density_estimation.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] 

> x <- library("KernSmooth")
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

> x <- library("flexmix")

  When sourcing 'Ch_density_estimation.R':
Error: there is no package called 'flexmix'
Execution halted
when running code in 'Ch_meta_analysis.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("rmeta")

  When sourcing 'Ch_meta_analysis.R':
Error: there is no package called 'rmeta'
Execution halted
when running code in 'Ch_multidimensional_scaling.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] 

> x <- library("ape")

  When sourcing 'Ch_multidimensional_scaling.R':
Error: there is no package called 'ape'
Execution halted
when running code in 'Ch_recursive_partitioning.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("vcd")

  When sourcing 'Ch_recursive_partitioning.R':
Error: there is no package called 'vcd'
Execution halted
when running code in 'Ch_simple_inference.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("vcd")

  When sourcing 'Ch_simple_inference.R':
Error: there is no package called 'vcd'
Execution halted
when running code in 'Ch_survival_analysis.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] 

> x <- library("survival")

> x <- library("coin")

  When sourcing 'Ch_survival_analysis.R':
Error: there is no package called 'coin'
Execution halted

  'Ch_analysing_longitudinal_dataI.Rnw' using 'UTF-8'... failed
  'Ch_analysing_longitudinal_dataII.Rnw' using 'UTF-8'... failed
  'Ch_analysis_of_variance.Rnw' using 'UTF-8'... OK
  'Ch_cluster_analysis.Rnw' using 'UTF-8'... failed
  'Ch_conditional_inference.Rnw' using 'UTF-8'... failed
  'Ch_density_estimation.Rnw' using 'UTF-8'... failed
  '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'... failed
  'Ch_multidimensional_scaling.Rnw' using 'UTF-8'... failed
  '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'... failed
  'Ch_simple_inference.Rnw' using 'UTF-8'... failed
  'Ch_survival_analysis.Rnw' using 'UTF-8'... failed
  'preface.Rnw' using 'UTF-8'... OK