* using log directory ‘/srv/hornik/tmp/CRAN_pretest/StroupGLMM.Rcheck’ * using R Under development (unstable) (2024-09-30 r87204) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘StroupGLMM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘StroupGLMM’ version ‘0.3.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/125s] NOTE Maintainer: ‘Muhammad Yaseen ’ Days since last update: 6 Found the following (possibly) invalid URLs: URL: https://www.gnu.org/licenses/gpl-3.0 From: README.md Status: Error Message: Connection timed out after 60001 milliseconds * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... 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OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [18s/18s] ERROR Running examples in ‘StroupGLMM-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Exam8.3 > ### Title: Example 8.3 from Generalized Linear Mixed Models: Modern > ### Concepts, Methods and Applications by Walter W. Stroup (p-255) > ### Aliases: Exam8.3 > > ### ** Examples > > > ## Response Surface Design with incomplete blocking (page 255) > data(DataSet8.3) Warning in data(DataSet8.3) : data set ‘DataSet8.3’ not found > DataSet8.3$block <- factor(x = DataSet8.3$block) > DataSet8.3$aa <- factor(x = DataSet8.3$a) > DataSet8.3$bb <- factor(x = DataSet8.3$b) > DataSet8.3$cc <- factor(x = DataSet8.3$c) > > library(lmerTest) Loading required package: lme4 Loading required package: Matrix Attaching package: ‘lmerTest’ The following object is masked from ‘package:lme4’: lmer The following object is masked from ‘package:stats’: step > library(lattice) > > Exam8.3.fm1 <- + lmer( + y ~ aa:bb:cc + a + b + c + + I(a^2) + I(b^2) + I(c^2) + + a*b + a*c + b*c + (1|block) + , data = DataSet8.3 + ) fixed-effect model matrix is rank deficient so dropping 24 columns / coefficients > > ##--- page 256 > anova(Exam8.3.fm1, ddf = "Kenward-Roger", type = 1) Type I Analysis of Variance Table with Kenward-Roger's method Sum Sq Mean Sq NumDF DenDF F value Pr(>F) a 40.960 40.960 1 12 19.1374 0.0009048 *** b 45.901 45.901 1 12 21.4458 0.0005791 *** c 4.306 4.306 1 12 2.0117 0.1815368 I(a^2) 22.103 22.103 1 3 10.3272 0.0488220 * I(b^2) 35.975 35.975 1 3 16.8084 0.0262537 * I(c^2) 1.495 1.495 1 3 0.6984 0.4646625 a:b 1.620 1.620 1 12 0.7569 0.4013689 a:c 2.205 2.205 1 12 1.0302 0.3301347 b:c 10.811 10.811 1 12 5.0512 0.0441960 * aa:bb:cc 1.441 0.480 3 12 0.2245 0.8775621 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > > Exam8.3.fm2 <- + lmer( + y ~ a + b + c + + I(a^2) + I(b^2) + I(c^2) + + a*b + a*c + b*c + (1|block) + , data = DataSet8.3 + ) > ##--- page 257 > anova(Exam8.3.fm2, ddf = "Kenward-Roger", type = 1) Type I Analysis of Variance Table with Kenward-Roger's method Sum Sq Mean Sq NumDF DenDF F value Pr(>F) a 40.960 40.960 1 15 22.6507 0.0002534 *** b 45.901 45.901 1 15 25.3828 0.0001471 *** c 4.306 4.306 1 15 2.3810 0.1436508 I(a^2) 18.675 18.675 1 3 10.3272 0.0488220 * I(b^2) 30.395 30.395 1 3 16.8084 0.0262537 * I(c^2) 1.263 1.263 1 3 0.6984 0.4646625 a:b 1.620 1.620 1 15 0.8959 0.3588953 a:c 2.205 2.205 1 15 1.2194 0.2868867 b:c 10.811 10.811 1 15 5.9786 0.0273022 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > ##--- page 257 > Exam8.3.fm3 <- + lmer( + y ~ a + b + c + + I(a^2) + I(b^2) + + a*c + b*c + (1|block) + , DataSet8.3 + ) > anova(Exam8.3.fm3, ddf = "Kenward-Roger", type = 1) Type I Analysis of Variance Table with Kenward-Roger's method Sum Sq Mean Sq NumDF DenDF F value Pr(>F) a 40.960 40.960 1 16 22.7991 0.0002067 *** b 45.901 45.901 1 16 25.5491 0.0001172 *** c 4.306 4.306 1 16 2.3966 0.1411506 I(a^2) 20.067 20.067 1 4 11.1695 0.0287800 * I(b^2) 32.660 32.660 1 4 18.1793 0.0130150 * a:c 2.205 2.205 1 16 1.2273 0.2843011 b:c 10.811 10.811 1 16 6.0177 0.0260104 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > ##--- scatter plot with regression plane by using Hoerl function ( page#233) > a <- seq(from = -1, to = 1, by = 1) > b <- seq(from = -1, to = 1, by = 1) > c <- seq(from = -1, to = 1, by = 1) > abc <- expand.grid(a = a, b = b, c = c) > > Yhat <- NULL > for(i in 1:nrow(abc)) { + Yhat[i] <- 50.08500 + 1.6*abc$a[i] + 1.69375*abc$b[i] + 0.51875*abc$c[i]- + 3.30250*I((abc$a[i])^2)-3.51500*I((abc$b)^2)[i] - + 0.52500*(abc$a)[i]*(abc$c)[i]-1.16250*(abc$b)[i]*(abc$c)[i] + } > > Newdata <- data.frame(abc, Yhat) > Plot1 <- + wireframe(Yhat ~ b*a, data = subset(Newdata,c==-1), + xlab = "b", ylab = "a", + main = "Predicte response surface at C=-1", colorkey = F, + drape = TRUE, scales = list(arrows = F),xlim=c(max(b),(min(b))), + screen = list(z = -50, x =-70) + ) Error in stopifnot(is.list(x), is.list(val)) : F used instead of FALSE Calls: wireframe ... cloud.formula -> updateList -> modifyList -> stopifnot Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE