* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/cold.Rcheck’ * using R Under development (unstable) (2025-11-21 r89046) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘cold/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cold’ version ‘2.0-3’ * package encoding: UTF-8 * 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 ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cold’ can be installed ... [10s/10s] OK * used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ * used Fortran compiler: ‘GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [15s/15s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking examples ... [13s/13s] OK * checking examples with --run-donttest ... [539s/542s] ERROR Running examples in ‘cold-Ex.R’ failed The error most likely occurred in: > ### Name: datacold > ### Title: Data > ### Aliases: datacold > ### Keywords: datasets > > ### ** Examples > > data(datacold) > > mod0<- cold(z~Time*Treatment, data=datacold, time="Time", + id="Subject", dependence="ind") > summary (mod0) Call: cold(formula = z ~ Time * Treatment, data = datacold, id = "Subject", time = "Time", dependence = "ind") Number of profiles in the dataset: 30 Number of profiles used in the fit: 30 Dependence structure: ind Log likelihood: -1074.015 AIC: 2156.031 Fixed effects: Estimate Std. Error z value p-value (Intercept) 1.4373024 0.03546160 40.531 0 Time 0.2737826 0.03744090 7.312 0 Treatment -0.3915651 0.05821677 -6.726 0 Time:Treatment 0.4060127 0.05945204 6.829 0 Message: 0 > > modI<- cold(z~Time*Treatment, data=datacold, time="Time", + id="Subject", dependence="AR1") > summary (modI) Call: cold(formula = z ~ Time * Treatment, data = datacold, id = "Subject", time = "Time", dependence = "AR1") Number of profiles in the dataset: 30 Number of profiles used in the fit: 30 Dependence structure: AR1 Log likelihood: -681.8906 AIC: 1373.781 Fixed effects: Estimate Std. Error z value p-value (Intercept) 1.3931913 0.08423103 16.540 0.000000 Time 0.2759878 0.05718272 4.826 0.000001 Treatment -0.2996408 0.12724192 -2.355 0.018528 Time:Treatment 0.3850335 0.08939539 4.307 0.000017 Estimated correlation parameter: rho Estimate Std. Error z value p-value 0.82824392 0.01571836 52.69300000 0.00000000 Message: 0 > > anova(mod0,modI) Data: datacold Model1: z ~ Time * Treatment dependence = ind Model2: z ~ Time * Treatment dependence = AR1 AIC BIC logLik Deviance df p-value Model1 2156.031 2171.896 -1074.0155 Model2 1373.781 1393.612 -681.8906 784.25 1 0 > > plot(modI,which=1,factor=Treatment,xlab="Time (weeks)", + ylab="Count", main="Model AR1") > > > ### independent with random intercept > mod0R <- cold(z ~ Time * Treatment, random = ~ 1, data = datacold, + time = "Time", id = "Subject", dependence = "indR") > summary(mod0R) Call: cold(formula = z ~ Time * Treatment, random = ~1, data = datacold, id = "Subject", time = "Time", dependence = "indR") Number of profiles in the dataset: 30 Number of profiles used in the fit: 30 Dependence structure: indR Log likelihood: -707.7146 AIC: 1425.429 Fixed effects: Estimate Std. Error z value p-value (Intercept) 1.0316222 0.27076993 3.810 0.000139 Time 0.2737779 0.03744061 7.312 0.000000 Treatment -0.3502961 0.38480028 -0.910 0.362647 Time:Treatment 0.4059789 0.05945172 6.829 0.000000 Random effects: Variance (Intercept) 1.062952 Message: 0 > > ### independent with random intercept (dependence="indR") > ### using cubature (integration = "cubature") > ## No test: > mod0R.C <- cold(z ~ Time * Treatment, random = ~ 1, data = datacold, + time = "Time", id = "Subject", dependence = "indR", integration = "cubature") > summary(mod0R.C) Call: cold(formula = z ~ Time * Treatment, random = ~1, data = datacold, id = "Subject", time = "Time", dependence = "indR", integration = "cubature") Number of profiles in the dataset: 30 Number of profiles used in the fit: 30 Dependence structure: indR Log likelihood: -718.6394 AIC: 1447.279 Fixed effects: Estimate Std. Error z value p-value (Intercept) 1.4373024 0.003706953 387.731 0.000000 Time 0.2737825 0.011597803 23.606 0.000000 Treatment -0.3915651 0.279395382 -1.401 0.161073 Time:Treatment 0.4060127 0.047445196 8.558 0.000000 Random effects: Variance (Intercept) 1 Message: 0 > > randeff(mod0R.C) (Intercept) 1 0.39598636 2 0.63799840 3 0.28265768 4 0.66564993 5 -2.93621815 6 -0.77673390 7 -1.32678023 8 1.10683312 9 -0.42391252 10 -2.42539252 11 -0.37126879 12 -1.26224171 13 0.09230395 14 -0.20618904 15 -0.08358672 16 0.85825918 17 -2.01342044 18 -26.34832242 19 -0.04397979 20 -0.02099028 21 -0.66968569 22 0.00148258 23 -1.16612258 24 0.27235753 25 -0.71413746 26 0.52555343 27 0.35370317 28 0.48527953 29 -0.86074093 30 0.57684672 > > ## End(No test) > > > ### dependence="indR2" > ## It takes a long time to run > ## No test: > > ## Using Monte Carlo method (integration = "MC") > mod0R2MC <- cold(z ~ Time * Treatment, ~ 1 + Time, datacold, time = "Time", + id = "Subject", dependence = "indR2", integration = "MC") > > summary (mod0R2MC) Call: cold(formula = z ~ Time * Treatment, random = ~1 + Time, data = datacold, id = "Subject", time = "Time", dependence = "indR2", integration = "MC") Number of profiles in the dataset: 30 Number of profiles used in the fit: 30 Dependence structure: indR2 Log likelihood: -701.3542 AIC: 1414.708 Fixed effects: Estimate Std. Error z value p-value (Intercept) 0.9704746 0.22665147 4.282 0.000019 Time 0.3652185 0.06974576 5.236 0.000000 Treatment -0.3262587 0.34013226 -0.959 0.337452 Time:Treatment 0.3226651 0.09758666 3.306 0.000945 Random effects: Variance (Intercept) 1.07725763 Time 0.02998478 Message: 0 > > randeff(mod0R2MC) (Intercept) Time 1 0.8911251 -0.26640865 2 1.1128876 -0.12790486 3 0.7797689 -0.29277032 4 1.1573434 -0.23233733 5 -5.8800064 3.29963004 6 -0.5861574 0.50096399 7 -0.9519486 0.17509598 8 1.6054136 -0.32176206 9 -0.1677560 0.39865325 10 -2.3289632 0.63315705 11 -0.2252914 0.56537039 12 -0.8800876 0.15859494 13 0.5502153 -0.05595602 14 0.2424766 -0.02291532 15 0.2312363 0.29638835 16 1.3222501 -0.13123902 17 -1.4183984 -0.64024548 18 -25.9468010 -0.68788367 19 0.3701760 -0.03135378 20 0.3102736 0.11069812 21 -0.2158148 -0.10971983 22 0.4082975 -0.01775117 23 -0.8124673 0.07452233 24 0.7028136 -0.06247109 25 -0.5059090 0.29008312 26 0.8076961 0.18576451 27 0.5572358 0.29642522 28 0.9075815 -0.04674011 29 -0.4935046 0.05187377 30 1.0727644 -0.20472991 > > ## Using cubature (integration = "cubature") > mod0R2C<-cold(z ~ Time * Treatment, random = ~ 1 + Time, data = datacold, + time = "Time", id = "Subject", dependence = "indR2", integration = "cubature") Warning in log(z[[1]] * (1/((2 * pi) * exp(omega1/2) * exp(omega2/2)))) : NaNs produced Warning in log(z[[1]] * (1/((2 * pi) * exp(omega1/2) * exp(omega2/2)))) : NaNs produced Warning in log(z[[1]] * (1/((2 * pi) * exp(omega1/2) * exp(omega2/2)))) : NaNs produced Error in optim(par = start, fn = LogL.pss0Ic2, gr = gradLogL.pss0Ic2, : initial value in 'vmmin' is not finite Calls: cold -> optim Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/cold.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 10:10.11, 592.79 + 13.84