* using log directory ‘/data/localhost/ripley/R/packages/tests-OpenBLAS/SynergyLMM.Rcheck’ * using R Under development (unstable) (2026-07-19 r90278) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-07-19 16:42:35 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘SynergyLMM/DESCRIPTION’ ... OK * this is package ‘SynergyLMM’ version ‘1.1.3’ * 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 ‘SynergyLMM’ can be installed ... OK * checking package directory ... OK * checking ‘build’ 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 whether startup messages can be suppressed ... OK * checking use of S3 registration ... 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 ... [12s/13s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [63s/67s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [126s/132s] [127s/132s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SynergyLMM) > > test_check("SynergyLMM") Normality Test of Random Effects $Time Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.9678 P VALUE: 0.8702 Description: Normality Test of Time random effects Normalized Residuals Levene Homoscedasticity Test by Sample Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 9 0.5417 0.8398 80 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Sample Fligner-Killeen test of homogeneity of variances data: normalized_resid by SampleID Fligner-Killeen:med chi-squared = 5.1645, df = 9, p-value = 0.8197 Normality Test of Random Effects $Time Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.9678 P VALUE: 0.8702 Description: Normality Test of Time random effects Normalized Residuals Levene Homoscedasticity Test by Sample Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 9 0.5417 0.8398 80 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Sample Fligner-Killeen test of homogeneity of variances data: normalized_resid by SampleID Fligner-Killeen:med chi-squared = 5.1645, df = 9, p-value = 0.8197 Normality Test of Random Effects $Time Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.9678 P VALUE: 0.8702 Description: Normality Test of Time random effects Normalized Residuals Levene Homoscedasticity Test by Sample Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 9 0.5417 0.8398 80 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Sample Fligner-Killeen test of homogeneity of variances data: normalized_resid by SampleID Fligner-Killeen:med chi-squared = 5.1645, df = 9, p-value = 0.8197 Normalized Residuals Normality Test Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.7822 P VALUE: 3.211e-10 Normalized Residuals Levene Homoscedasticity Test by Time Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 8 0.5553 0.8111 81 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time Fligner-Killeen test of homogeneity of variances data: normalized_resid by as.factor(Time) Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825 Normalized Residuals Levene Homoscedasticity Test by Treatment Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 3 0.9028 0.4433 86 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment Fligner-Killeen test of homogeneity of variances data: normalized_resid by Treatment Fligner-Killeen:med chi-squared = 1.5827, df = 3, p-value = 0.6633 Outlier observations SampleID Time Treatment TV RTV logRTV TV0 normalized_resid 90 10 9 Drug_A 1000 8.342366 2.121347 119.8701 6.124042 Normalized Residuals Normality Test Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.7822 P VALUE: 3.211e-10 Normalized Residuals Levene Homoscedasticity Test by Time Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 8 0.5553 0.8111 81 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time Fligner-Killeen test of homogeneity of variances data: normalized_resid by as.factor(Time) Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825 Normalized Residuals Levene Homoscedasticity Test by Treatment Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 3 0.9028 0.4433 86 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment Fligner-Killeen test of homogeneity of variances data: normalized_resid by Treatment Fligner-Killeen:med chi-squared = 1.5827, df = 3, p-value = 0.6633 Outlier observations SampleID Time Treatment TV RTV logRTV TV0 normalized_resid 90 10 9 Drug_A 1000 8.342366 2.121347 119.8701 6.124042 Normalized Residuals Normality Test Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.7822 P VALUE: 3.211e-10 Normalized Residuals Levene Homoscedasticity Test by Time Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 8 0.5553 0.8111 81 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time Fligner-Killeen test of homogeneity of variances data: normalized_resid by as.factor(Time) Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825 Normalized Residuals Levene Homoscedasticity Test by Treatment Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 3 0.9028 0.4433 86 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment Fligner-Killeen test of homogeneity of variances data: normalized_resid by Treatment Fligner-Killeen:med chi-squared = 1.5827, df = 3, p-value = 0.6633 Outlier observations SampleID Time Treatment TV RTV logRTV TV0 normalized_resid 90 10 9 Drug_A 1000 8.342366 2.121347 119.8701 6.124042 Normalized Residuals Normality Test Title: Shapiro - Wilk Normality Test Test Results: STATISTIC: W: 0.7822 P VALUE: 3.211e-10 Normalized Residuals Levene Homoscedasticity Test by Time Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 8 0.5553 0.8111 81 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time Fligner-Killeen test of homogeneity of variances data: normalized_resid by as.factor(Time) Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825 Normalized Residuals Levene Homoscedasticity Test by Treatment Levene's Test for Homogeneity of Variance (center = median) Df F value Pr(>F) group 3 0.9028 0.4433 86 Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment Fligner-Killeen test of homogeneity of variances data: normalized_resid by Treatment Fligner-Killeen:med chi-squared = 1.5827, df = 3, p-value = 0.6633 Outlier observations SampleID Time Treatment TV RTV logRTV TV0 normalized_resid 90 10 9 Drug_A 1000 8.342366 2.121347 119.8701 6.124042 Random effect variances not available. Returned R2 does not account for random effects. Random effect variances not available. Returned R2 does not account for random effects. No subject with a log-likelihood displacement greater than: 3.976 [1] "Outliers with Log Likelihood displacement greater than: 4.977" 4 6.554489 [1] "Outliers with Log Likelihood displacement greater than: -1000" 1 2 3 4 5 6 7 0.08258159 2.00421829 3.20399631 1.04719077 0.29520400 1.85948923 3.28403183 8 9 10 1.09210541 0.36262353 0.02277539 No subject with a Cook's distance greater than: 0.919 No subject with a Cook's distance greater than: 0.582 [1] "Subjects with Cook's distance greater than: -10" 1 2 3 4 5 6 0.0097363880 0.4406576193 0.8019684428 0.2264886706 0.0670661290 0.4616129833 7 8 9 10 0.8019684428 0.2264886706 0.0256954978 0.0002433785 `geom_line()`: Each group consists of only one observation. i Do you need to adjust the group aesthetic? Some Combination Index values were infinite (+Inf) due to zero denominators for time: 1. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 2. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 3. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 4. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 5. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 6. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 7. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 8. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 9. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 1. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 2. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 3. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 4. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 5. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 6. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 7. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 8. These values have been capped at a maximum of 100 to preserve interpretability. Some Combination Index values were infinite (+Inf) due to zero denominators for time: 9. These values have been capped at a maximum of 100 to preserve interpretability. Saving _problems/test-lmmSynergy-442.R [ FAIL 1 | WARN 1709 | SKIP 0 | PASS 324 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-lmmSynergy.R:441:3'): Test lmmSynergy prints warning message if p-value = 0 ── Expected `lmmSynergy(model, method = "RA", nsim = 10)` to throw a warning. [ FAIL 1 | WARN 1709 | SKIP 0 | PASS 324 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [131s/135s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-OpenBLAS/SynergyLMM.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:50.79, 378.34 + 9.18