CRAN Package Check Results for Package HSAUR2

Last updated on 2022-01-27 11:51:23 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-18 3.90 193.28 197.18 OK
r-devel-linux-x86_64-debian-gcc 1.1-18 3.10 152.25 155.35 OK
r-devel-linux-x86_64-fedora-clang 1.1-18 279.75 OK
r-devel-linux-x86_64-fedora-gcc 1.1-18 275.13 OK
r-devel-windows-x86_64-new-UL 1.1-18 122.00 81.00 203.00 OK --no-vignettes
r-devel-windows-x86_64-new-TK 1.1-18 WARN
r-patched-linux-x86_64 1.1-18 5.39 196.49 201.88 OK
r-release-linux-x86_64 1.1-18 3.11 196.78 199.89 OK
r-release-macos-arm64 1.1-18 OK
r-release-macos-x86_64 1.1-18 OK
r-release-windows-ix86+x86_64 1.1-18 10.00 50.00 60.00 OK --no-vignettes
r-oldrel-macos-x86_64 1.1-18 OK
r-oldrel-windows-ix86+x86_64 1.1-18 8.00 44.00 52.00 OK --no-vignettes

Check Details

Version: 1.1-18
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'lme4'
Flavor: r-devel-windows-x86_64-new-TK

Version: 1.1-18
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,
    + show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED]
    
    > HSAURpkg <- require("HSAUR2")
    Loading required package: HSAUR2
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))
    
    > rm(HSAURpkg)
    
    > a <- Sys.setlocale("LC_ALL", "C")
    
    > book <- TRUE
    
    > refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA",
    + "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC",
    + "MA", "PCA", "MDS ..." ... [TRUNCATED]
    
    > ch <- function(x) {
    + ch <- refs[which(refs[, 1] == x), ]
    + if (book) {
    + return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
    + .... [TRUNCATED]
    
    > if (file.exists("deparse.R")) source("deparse.R")
    
    > setHook(packageEvent("lattice", "attach"), function(...) {
    + lattice.options(default.theme = function() standard.theme("pdf",
    + color = .... [TRUNCATED]
    
    > book <- FALSE
    
    > 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,
    + show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED]
    
    > HSAURpkg <- require("HSAUR2")
    Loading required package: HSAUR2
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))
    
    > rm(HSAURpkg)
    
    > a <- Sys.setlocale("LC_ALL", "C")
    
    > book <- TRUE
    
    > refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA",
    + "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC",
    + "MA", "PCA", "MDS ..." ... [TRUNCATED]
    
    > ch <- function(x) {
    + ch <- refs[which(refs[, 1] == x), ]
    + if (book) {
    + return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
    + .... [TRUNCATED]
    
    > if (file.exists("deparse.R")) source("deparse.R")
    
    > setHook(packageEvent("lattice", "attach"), function(...) {
    + lattice.options(default.theme = function() standard.theme("pdf",
    + color = .... [TRUNCATED]
    
    > book <- FALSE
    
    > options(digits = 3)
    
    > if (!interactive()) {
    + print.summary.gee <- function(x, digits = NULL, quote = FALSE,
    + prefix = "", ...) {
    + if (is.null(digi .... [TRUNCATED]
    
    > library("gee")
    
    > data("BtheB", package = "HSAUR2")
    
    > BtheB$subject <- factor(rownames(BtheB))
    
    > nobs <- nrow(BtheB)
    
    > BtheB_long <- reshape(BtheB, idvar = "subject", varying = c("bdi.2m",
    + "bdi.3m", "bdi.5m", "bdi.8m"), direction = "long")
    
    > BtheB_long$time <- rep(c(2, 3, 5, 8), rep(nobs, 4))
    
    > names(BtheB_long)[names(BtheB_long) == "treatment"] <- "trt"
    
    > osub <- order(as.integer(BtheB_long$subject))
    
    > BtheB_long <- BtheB_long[osub, ]
    
    > btb_gee <- gee(bdi ~ bdi.pre + trt + length + drug,
    + data = BtheB_long, id = subject, family = gaussian, corstr = "independence")
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
    (Intercept) bdi.pre trtBtheB length>6m drugYes
     3.569 0.582 -3.237 1.458 -3.741
    
    > btb_gee1 <- gee(bdi ~ bdi.pre + trt + length + drug,
    + data = BtheB_long, id = subject, family = gaussian, corstr = "exchangeable")
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
    (Intercept) bdi.pre trtBtheB length>6m drugYes
     3.569 0.582 -3.237 1.458 -3.741
    
    > summary(btb_gee)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Identity
     Variance to Mean Relation: Gaussian
     Correlation Structure: Independent
    
    Call:
    gee(formula = bdi ~ bdi.pre + trt + length + drug, id = subject,
     data = BtheB_long, family = gaussian, corstr = "independence")
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -21.650 -5.849 0.113 5.584 28.187
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) 3.569 1.4833 2.41 2.2695 1.572
    bdi.pre 0.582 0.0564 10.32 0.0916 6.355
    trtBtheB -3.237 1.1296 -2.87 1.7746 -1.824
    length>6m 1.458 1.1380 1.28 1.4826 0.983
    drugYes -3.741 1.1766 -3.18 1.7827 -2.099
    
    Estimated Scale Parameter: 79.3
    Number of Iterations: 1
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1 0 0 0
    [2,] 0 1 0 0
    [3,] 0 0 1 0
    [4,] 0 0 0 1
    
    > summary(btb_gee1)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Identity
     Variance to Mean Relation: Gaussian
     Correlation Structure: Exchangeable
    
    Call:
    gee(formula = bdi ~ bdi.pre + trt + length + drug, id = subject,
     data = BtheB_long, family = gaussian, corstr = "exchangeable")
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -23.96 -6.64 -1.11 4.26 25.45
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) 3.023 2.3039 1.3122 2.2320 1.3544
    bdi.pre 0.648 0.0823 7.8741 0.0835 7.7583
    trtBtheB -2.169 1.7664 -1.2281 1.7361 -1.2495
    length>6m -0.111 1.7309 -0.0643 1.5509 -0.0718
    drugYes -3.000 1.8257 -1.6430 1.7316 -1.7323
    
    Estimated Scale Parameter: 81.7
    Number of Iterations: 5
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1.000 0.676 0.676 0.676
    [2,] 0.676 1.000 0.676 0.676
    [3,] 0.676 0.676 1.000 0.676
    [4,] 0.676 0.676 0.676 1.000
    
    > data("respiratory", package = "HSAUR2")
    
    > resp <- subset(respiratory, month > "0")
    
    > resp$baseline <- rep(subset(respiratory, month ==
    + "0")$status, rep(4, 111))
    
    > resp$nstat <- as.numeric(resp$status == "good")
    
    > resp$month <- resp$month[, drop = TRUE]
    
    > names(resp)[names(resp) == "treatment"] <- "trt"
    
    > levels(resp$trt)[2] <- "trt"
    
    > resp_glm <- glm(status ~ centre + trt + gender + baseline +
    + age, data = resp, family = "binomial")
    
    > resp_gee1 <- gee(nstat ~ centre + trt + gender + baseline +
    + age, data = resp, family = "binomial", id = subject, corstr = "independence",
    + .... [TRUNCATED]
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
     (Intercept) centre2 trttrt gendermale
     -0.9002 0.6716 1.2992 0.1192
    baselinegood age
     1.8820 -0.0182
    
    > resp_gee2 <- gee(nstat ~ centre + trt + gender + baseline +
    + age, data = resp, family = "binomial", id = subject, corstr = "exchangeable",
    + .... [TRUNCATED]
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
     (Intercept) centre2 trttrt gendermale
     -0.9002 0.6716 1.2992 0.1192
    baselinegood age
     1.8820 -0.0182
    
    > summary(resp_glm)
    
    Call:
    glm(formula = status ~ centre + trt + gender + baseline + age,
     family = "binomial", data = resp)
    
    Deviance Residuals:
     Min 1Q Median 3Q Max
    -2.315 -0.855 0.434 0.895 1.925
    
    Coefficients:
     Estimate Std. Error z value Pr(>|z|)
    (Intercept) -0.90017 0.33765 -2.67 0.0077
    centre2 0.67160 0.23957 2.80 0.0051
    trttrt 1.29922 0.23684 5.49 4.1e-08
    gendermale 0.11924 0.29467 0.40 0.6857
    baselinegood 1.88203 0.24129 7.80 6.2e-15
    age -0.01817 0.00886 -2.05 0.0404
    
    (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 608.93 on 443 degrees of freedom
    Residual deviance: 483.22 on 438 degrees of freedom
    AIC: 495.2
    
    Number of Fisher Scoring iterations: 4
    
    
    > summary(resp_gee1)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Logit
     Variance to Mean Relation: Binomial
     Correlation Structure: Independent
    
    Call:
    gee(formula = nstat ~ centre + trt + gender + baseline + age,
     id = subject, data = resp, family = "binomial", corstr = "independence",
     scale.fix = TRUE, scale.value = 1)
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -0.9313 -0.3062 0.0897 0.3302 0.8431
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) -0.9002 0.33765 -2.666 0.460 -1.956
    centre2 0.6716 0.23957 2.803 0.357 1.882
    trttrt 1.2992 0.23684 5.486 0.351 3.704
    gendermale 0.1192 0.29467 0.405 0.443 0.269
    baselinegood 1.8820 0.24129 7.800 0.350 5.376
    age -0.0182 0.00886 -2.049 0.013 -1.397
    
    Estimated Scale Parameter: 1
    Number of Iterations: 1
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1 0 0 0
    [2,] 0 1 0 0
    [3,] 0 0 1 0
    [4,] 0 0 0 1
    
    > summary(resp_gee2)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Logit
     Variance to Mean Relation: Binomial
     Correlation Structure: Exchangeable
    
    Call:
    gee(formula = nstat ~ centre + trt + gender + baseline + age,
     id = subject, data = resp, family = "binomial", corstr = "exchangeable",
     scale.fix = TRUE, scale.value = 1)
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -0.9313 -0.3062 0.0897 0.3302 0.8431
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) -0.9002 0.4785 -1.881 0.460 -1.956
    centre2 0.6716 0.3395 1.978 0.357 1.882
    trttrt 1.2992 0.3356 3.871 0.351 3.704
    gendermale 0.1192 0.4176 0.286 0.443 0.269
    baselinegood 1.8820 0.3419 5.504 0.350 5.376
    age -0.0182 0.0126 -1.446 0.013 -1.397
    
    Estimated Scale Parameter: 1
    Number of Iterations: 1
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1.000 0.336 0.336 0.336
    [2,] 0.336 1.000 0.336 0.336
    [3,] 0.336 0.336 1.000 0.336
    [4,] 0.336 0.336 0.336 1.000
    
    > se <- summary(resp_gee2)$coefficients["trttrt", "Robust S.E."]
    
    > coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975)
    [1] 0.612 1.987
    
    > exp(coef(resp_gee2)["trttrt"] + c(-1, 1) * se * qnorm(0.975))
    [1] 1.84 7.29
    
    > data("epilepsy", package = "HSAUR2")
    
    > itp <- interaction(epilepsy$treatment, epilepsy$period)
    
    > tapply(epilepsy$seizure.rate, itp, mean)
     placebo.1 Progabide.1 placebo.2 Progabide.2 placebo.3
     9.36 8.58 8.29 8.42 8.79
    Progabide.3 placebo.4 Progabide.4
     8.13 7.96 6.71
    
    > tapply(epilepsy$seizure.rate, itp, var)
     placebo.1 Progabide.1 placebo.2 Progabide.2 placebo.3
     102.8 332.7 66.7 140.7 215.3
    Progabide.3 placebo.4 Progabide.4
     193.0 58.2 126.9
    
    > layout(matrix(1:2, nrow = 1))
    
    > ylim <- range(epilepsy$seizure.rate)
    
    > placebo <- subset(epilepsy, treatment == "placebo")
    
    > progabide <- subset(epilepsy, treatment == "Progabide")
    
    > boxplot(seizure.rate ~ period, data = placebo, ylab = "Number of seizures",
    + xlab = "Period", ylim = ylim, main = "Placebo")
    
    > boxplot(seizure.rate ~ period, data = progabide, main = "Progabide",
    + ylab = "Number of seizures", xlab = "Period", ylim = ylim)
    
    > layout(matrix(1:2, nrow = 1))
    
    > ylim <- range(log(epilepsy$seizure.rate + 1))
    
    > boxplot(log(seizure.rate + 1) ~ period, data = placebo,
    + main = "Placebo", ylab = "Log number of seizures", xlab = "Period",
    + ylim = yli .... [TRUNCATED]
    
    > boxplot(log(seizure.rate + 1) ~ period, data = progabide,
    + main = "Progabide", ylab = "Log number of seizures", xlab = "Period",
    + ylim = .... [TRUNCATED]
    
    > per <- rep(log(2), nrow(epilepsy))
    
    > epilepsy$period <- as.numeric(epilepsy$period)
    
    > names(epilepsy)[names(epilepsy) == "treatment"] <- "trt"
    
    > fm <- seizure.rate ~ base + age + trt + offset(per)
    
    > epilepsy_glm <- glm(fm, data = epilepsy, family = "poisson")
    
    > epilepsy_gee1 <- gee(fm, data = epilepsy, family = "poisson",
    + id = subject, corstr = "independence", scale.fix = TRUE,
    + scale.value = 1 .... [TRUNCATED]
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
     (Intercept) base age trtProgabide
     -0.1306 0.0227 0.0227 -0.1527
    
    > epilepsy_gee2 <- gee(fm, data = epilepsy, family = "poisson",
    + id = subject, corstr = "exchangeable", scale.fix = TRUE,
    + scale.value = 1 .... [TRUNCATED]
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
     (Intercept) base age trtProgabide
     -0.1306 0.0227 0.0227 -0.1527
    
    > epilepsy_gee3 <- gee(fm, data = epilepsy, family = "poisson",
    + id = subject, corstr = "exchangeable", scale.fix = FALSE,
    + scale.value = .... [TRUNCATED]
    Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
    running glm to get initial regression estimate
     (Intercept) base age trtProgabide
     -0.1306 0.0227 0.0227 -0.1527
    
    > summary(epilepsy_glm)
    
    Call:
    glm(formula = fm, family = "poisson", data = epilepsy)
    
    Deviance Residuals:
     Min 1Q Median 3Q Max
    -4.436 -1.403 -0.503 0.484 12.322
    
    Coefficients:
     Estimate Std. Error z value Pr(>|z|)
    (Intercept) -0.130616 0.135619 -0.96 0.3355
    base 0.022652 0.000509 44.48 < 2e-16
    age 0.022740 0.004024 5.65 1.6e-08
    trtProgabide -0.152701 0.047805 -3.19 0.0014
    
    (Dispersion parameter for poisson family taken to be 1)
    
     Null deviance: 2521.75 on 235 degrees of freedom
    Residual deviance: 958.46 on 232 degrees of freedom
    AIC: 1732
    
    Number of Fisher Scoring iterations: 5
    
    
    > summary(epilepsy_gee1)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Logarithm
     Variance to Mean Relation: Poisson
     Correlation Structure: Independent
    
    Call:
    gee(formula = fm, id = subject, data = epilepsy, family = "poisson",
     corstr = "independence", scale.fix = TRUE, scale.value = 1)
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -4.920 0.181 1.707 4.885 69.966
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) -0.1306 0.135619 -0.963 0.36515 -0.358
    base 0.0227 0.000509 44.476 0.00124 18.332
    age 0.0227 0.004024 5.651 0.01158 1.964
    trtProgabide -0.1527 0.047805 -3.194 0.17111 -0.892
    
    Estimated Scale Parameter: 1
    Number of Iterations: 1
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1 0 0 0
    [2,] 0 1 0 0
    [3,] 0 0 1 0
    [4,] 0 0 0 1
    
    > summary(epilepsy_gee2)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Logarithm
     Variance to Mean Relation: Poisson
     Correlation Structure: Exchangeable
    
    Call:
    gee(formula = fm, id = subject, data = epilepsy, family = "poisson",
     corstr = "exchangeable", scale.fix = TRUE, scale.value = 1)
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -4.920 0.181 1.707 4.885 69.966
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) -0.1306 0.200442 -0.652 0.36515 -0.358
    base 0.0227 0.000753 30.093 0.00124 18.332
    age 0.0227 0.005947 3.824 0.01158 1.964
    trtProgabide -0.1527 0.070655 -2.161 0.17111 -0.892
    
    Estimated Scale Parameter: 1
    Number of Iterations: 1
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1.000 0.395 0.395 0.395
    [2,] 0.395 1.000 0.395 0.395
    [3,] 0.395 0.395 1.000 0.395
    [4,] 0.395 0.395 0.395 1.000
    
    > summary(epilepsy_gee3)
    
     GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
     gee S-function, version 4.13 modified 98/01/27 (1998)
    
    Model:
     Link: Logarithm
     Variance to Mean Relation: Poisson
     Correlation Structure: Exchangeable
    
    Call:
    gee(formula = fm, id = subject, data = epilepsy, family = "poisson",
     corstr = "exchangeable", scale.fix = FALSE, scale.value = 1)
    
    Summary of Residuals:
     Min 1Q Median 3Q Max
    -4.920 0.181 1.707 4.885 69.966
    
    
    Coefficients:
     Estimate Naive S.E. Naive z Robust S.E. Robust z
    (Intercept) -0.1306 0.4522 -0.289 0.36515 -0.358
    base 0.0227 0.0017 13.339 0.00124 18.332
    age 0.0227 0.0134 1.695 0.01158 1.964
    trtProgabide -0.1527 0.1594 -0.958 0.17111 -0.892
    
    Estimated Scale Parameter: 5.09
    Number of Iterations: 1
    
    Working Correlation
     [,1] [,2] [,3] [,4]
    [1,] 1.000 0.395 0.395 0.395
    [2,] 0.395 1.000 0.395 0.395
    [3,] 0.395 0.395 1.000 0.395
    [4,] 0.395 0.395 0.395 1.000
    
    > library("lme4")
    
     When sourcing 'Ch_analysing_longitudinal_dataII.R':
    Error: there is no package called 'lme4'
    Execution halted
    when running code in 'Ch_simultaneous_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,
    + show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED]
    
    > HSAURpkg <- require("HSAUR2")
    Loading required package: HSAUR2
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))
    
    > rm(HSAURpkg)
    
    > a <- Sys.setlocale("LC_ALL", "C")
    
    > book <- TRUE
    
    > refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA",
    + "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC",
    + "MA", "PCA", "MDS ..." ... [TRUNCATED]
    
    > ch <- function(x) {
    + ch <- refs[which(refs[, 1] == x), ]
    + if (book) {
    + return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
    + .... [TRUNCATED]
    
    > if (file.exists("deparse.R")) source("deparse.R")
    
    > setHook(packageEvent("lattice", "attach"), function(...) {
    + lattice.options(default.theme = function() standard.theme("pdf",
    + color = .... [TRUNCATED]
    
    > book <- FALSE
    
    > library("multcomp")
    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
    
    
    > library("coin")
    
    > library("sandwich")
    
    > library("lme4")
    
     When sourcing 'Ch_simultaneous_inference.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'... failed
     '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_gam.Rnw' using 'UTF-8'... OK
     'Ch_graphical_display.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_simultaneous_inference.Rnw' using 'UTF-8'... failed
     'Ch_survival_analysis.Rnw' using 'UTF-8'... OK
Flavor: r-devel-windows-x86_64-new-TK

Version: 1.1-18
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: HSAUR2
    Loading required package: tools
    
    Error: processing vignette 'Ch_analysing_longitudinal_dataI.Rnw' failed with diagnostics:
     chunk 3 (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: 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
    
    Error: processing vignette 'Ch_analysing_longitudinal_dataII.Rnw' failed with diagnostics:
     chunk 26 (label = ALDII-respiratory-lmer)
    Error in library("lme4") : there is no package called 'lme4'
    
    --- 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 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: 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 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: 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 1.8-38. For overview type 'help("mgcv-package")'.
    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 4.6-14
    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
    
    
    Error: processing vignette 'Ch_simultaneous_inference.Rnw' failed with diagnostics:
     chunk 3 (label = SIMC-setup)
    Error in library("lme4") : there is no package called 'lme4'
    
    --- 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_dataI.Rnw'
     'Ch_analysing_longitudinal_dataII.Rnw'
     'Ch_simultaneous_inference.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-new-TK