CRAN Package Check Results for Package HSAUR3

Last updated on 2022-01-17 11:05:37 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0-12 4.21 231.68 235.89 OK
r-devel-linux-x86_64-debian-gcc 1.0-12 2.99 180.45 183.44 OK
r-devel-linux-x86_64-fedora-clang 1.0-12 332.34 OK
r-devel-linux-x86_64-fedora-gcc 1.0-12 320.72 OK
r-devel-windows-x86_64-new-UL 1.0-12 183.00 114.00 297.00 OK --no-vignettes
r-devel-windows-x86_64-new-TK 1.0-12 WARN
r-patched-linux-x86_64 1.0-12 4.00 233.53 237.53 OK
r-release-linux-x86_64 1.0-12 OK
r-release-macos-arm64 1.0-12 OK
r-release-macos-x86_64 1.0-12 OK
r-release-windows-ix86+x86_64 1.0-12 8.00 70.00 78.00 OK --no-vignettes
r-oldrel-macos-x86_64 1.0-12 OK
r-oldrel-windows-ix86+x86_64 1.0-12 8.00 71.00 79.00 OK --no-vignettes

Check Details

Version: 1.0-12
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'lme4'
Flavor: r-devel-windows-x86_64-new-TK

Version: 1.0-12
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("HSAUR3")
    Loading required package: HSAUR3
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3"))
    
    > 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("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("HSAUR3")
    Loading required package: HSAUR3
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3"))
    
    > 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 = "HSAUR3")
    
    > 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 = "HSAUR3")
    
    > 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 = "HSAUR3")
    
    > 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("HSAUR3")
    Loading required package: HSAUR3
    Loading required package: tools
    
    > if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR3"))
    
    > 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
    
    The following object is masked from 'package:HSAUR3':
    
     birds
    
    
    > 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_bayesian_inference.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_missing_values.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_quantile_regression.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: 1.0-12
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: HSAUR3
    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: 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
    
    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: 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 5.4.9
    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: 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
    --- finished 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 5.4.9
    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: 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 1.8-38. 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: HSAUR3
    Loading required package: tools
    Checking rgeos availability: TRUE
    Please note that 'maptools' will be retired by the end of 2023,
    plan transition at your earliest convenience;
    some functionality will be moved to 'sp'.
    --- 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
    
    Attaching package: 'mice'
    
    The following object is masked from 'package:HSAUR3':
    
     toenail
    
    The following object is masked from 'package:stats':
    
     filter
    
    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
    --- 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
    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
    
    
    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: 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 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