* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/buildmer.Rcheck’ * using R Under development (unstable) (2025-02-14 r87716) * 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 * using option ‘--no-stop-on-test-error’ * checking for file ‘buildmer/DESCRIPTION’ ... OK * this is package ‘buildmer’ version ‘2.11’ * 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 ‘buildmer’ can be installed ... [19s/23s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/buildmer-00install.html' for details. * 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 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 ... [28s/35s] 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 ... [26s/35s] ERROR Running examples in ‘buildmer-Ex.R’ failed The error most likely occurred in: > ### Name: buildmer > ### Title: Use 'buildmer' to fit mixed-effects models using 'lmer'/'glmer' > ### from 'lme4' > ### Aliases: buildmer > > ### ** Examples > > library(buildmer) > model <- buildmer(Reaction ~ Days + (Days|Subject),lme4::sleepstudy) Determining predictor order Fitting via lm: Reaction ~ 1 Currently evaluating LRT for: Days Fitting via lm: Reaction ~ 1 + Days Updating formula: Reaction ~ 1 + Days Fitting via gam, with REML: Reaction ~ 1 + Days Currently evaluating LRT for: 1 | Subject Fitting via lmer, with REML: Reaction ~ 1 + Days + (1 | Subject) Ending the ordering procedure due to having reached the maximal feasible model - all higher models failed to converge. The types of convergence failure are: Optimizer reports not having finished (-2) Fitting ML reference model Fitting via lm: Reaction ~ 1 + Days Testing terms Fitting via lm: Reaction ~ 1 grouping term block score Iteration LRT 1 <NA> 1 NA NA 1 NA 1 NA 2 <NA> Days NA NA Days -32.673 1 6.460934e-15 All terms are significant > > # Tests from github issue #2, that also show the use of the 'direction' and 'crit' parameters: > bm.test <- buildmer(cbind(incidence,size - incidence) ~ period + (1 | herd), + family=binomial,data=lme4::cbpp) Determining predictor order Fitting via glm: cbind(incidence, size - incidence) ~ 1 Currently evaluating LRT for: period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Updating formula: cbind(incidence, size - incidence) ~ 1 + period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Currently evaluating LRT for: 1 | herd Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Updating formula: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Fitting ML and REML reference models Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Testing terms Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + (1 | herd) Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period grouping term block score Iteration LRT 1 <NA> 1 NA NA 1 NA 1 NA 2 <NA> period NA NA period -18.706656 1 1.151006e-05 3 herd 1 NA herd 1 -9.303008 1 9.114967e-05 All terms are significant > bm.test <- buildmer(cbind(incidence,size - incidence) ~ period + (1 | herd), + family=binomial,data=lme4::cbpp,buildmerControl=buildmerControl(direction='forward')) Determining predictor order Fitting via glm: cbind(incidence, size - incidence) ~ 1 Currently evaluating LRT for: period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Updating formula: cbind(incidence, size - incidence) ~ 1 + period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Currently evaluating LRT for: 1 | herd Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Updating formula: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) grouping term block score 1 <NA> 1 NA NA 1 NA 2 <NA> period NA NA period 7.512809e-09 3 herd 1 NA herd 1 9.114967e-05 Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) > bm.test <- buildmer(cbind(incidence,size - incidence) ~ period + (1 | herd), + family=binomial,data=lme4::cbpp,buildmerControl=buildmerControl(crit='AIC')) Determining predictor order Fitting via glm: cbind(incidence, size - incidence) ~ 1 Currently evaluating AIC for: period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Updating formula: cbind(incidence, size - incidence) ~ 1 + period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Currently evaluating AIC for: 1 | herd Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Updating formula: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Fitting ML and REML reference models Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Testing terms Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + (1 | herd) Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period grouping term block score Iteration AIC 1 <NA> 1 NA NA 1 NA 1 NA 2 <NA> period NA NA period -34.71577 1 -19.60994 3 herd 1 NA herd 1 -12.00527 1 -12.00527 All terms are significant > bm.test <- buildmer(cbind(incidence,size - incidence) ~ period + (1 | herd), + family=binomial,data=lme4::cbpp, + buildmerControl=buildmerControl(direction='forward',crit='AIC')) Determining predictor order Fitting via glm: cbind(incidence, size - incidence) ~ 1 Currently evaluating AIC for: period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Updating formula: cbind(incidence, size - incidence) ~ 1 + period Fitting via glm: cbind(incidence, size - incidence) ~ 1 + period Currently evaluating AIC for: 1 | herd Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) Updating formula: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) grouping term block score 1 <NA> 1 NA NA 1 NA 2 <NA> period NA NA period -34.71577 3 herd 1 NA herd 1 -12.00527 Fitting via glmer, with ML: cbind(incidence, size - incidence) ~ 1 + period + (1 | herd) > > # Example showing use of the 'include' parameter to force a particular term into the model > m1 <- buildmer(Reaction ~ Days,data=lme4::sleepstudy,buildmerControl=list(include=~(1|Subject))) Determining predictor order Fitting via lmer, with ML: Reaction ~ 1 + (1 | Subject) Convergence failure. Reducing terms and retrying... The failure was: Optimizer reports not having finished (-2) Error in reduce.model(p, conv) : No terms left for reduction, giving up Calls: buildmer ... buildmer.fit -> do.call -> order -> reorder -> reduce.model Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [19s/25s] ERROR Running ‘testthat.R’ [18s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(buildmer) > test_check('buildmer') grouping term block score Iteration LRT 1 <NA> 1 NA NA 1 NA 1 NA 2 Sex:Age:Eth:Lrn 1 NA Sex:Age:Eth:Lrn 1 -8.86362 1 0.0001414421 grouping term block score Iteration 1 NA 1 NA NA 1 NA 1 5 NA Eth NA NA Eth -7.3418284 1 3 NA Age NA NA Age -4.3688050 1 7 NA Age:Eth NA NA Age:Eth -4.5213739 1 9 NA Lrn NA NA Lrn -1.4747812 1 2 NA Sex NA NA Sex -0.7363892 1 4 NA Sex:Age NA NA Sex:Age -5.8421931 1 11 NA Age:Lrn NA NA Age:Lrn -2.3115461 1 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 1 8 NA Sex:Age:Eth NA NA Sex:Age:Eth -0.4237551 1 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 1 15 NA Age:Eth:Lrn NA NA Age:Eth:Lrn -5.0436262 1 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 1 12 NA Sex:Age:Lrn NA NA Sex:Age:Lrn -3.4094829 1 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 1 16 NA Sex:Age:Eth:Lrn NA NA Sex:Age:Eth:Lrn -0.7019217 1 LRT 1 NA 5 NA 3 NA 7 NA 9 NA 2 NA 4 NA 11 NA 6 NA 8 NA 13 NA 15 NA 10 NA 12 NA 14 NA 16 0.4956319 grouping term block score Iteration LRT 1 NA 1 NA NA 1 NA 2 NA 5 NA Eth NA NA Eth -7.3418284 2 NA 3 NA Age NA NA Age -4.3688050 2 NA 7 NA Age:Eth NA NA Age:Eth -4.5213739 2 NA 9 NA Lrn NA NA Lrn -1.4747812 2 NA 2 NA Sex NA NA Sex -0.7363892 2 NA 4 NA Sex:Age NA NA Sex:Age -5.8421931 2 NA 11 NA Age:Lrn NA NA Age:Lrn -2.3115461 2 NA 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 2 NA 8 NA Sex:Age:Eth NA NA Sex:Age:Eth -0.4237551 2 0.44347867 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 2 NA 15 NA Age:Eth:Lrn NA NA Age:Eth:Lrn -5.0436262 2 0.05044914 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 2 NA 12 NA Sex:Age:Lrn NA NA Sex:Age:Lrn -3.4094829 2 0.04329922 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 2 0.10713888 grouping term block score Iteration LRT 1 NA 1 NA NA 1 NA 3 NA 5 NA Eth NA NA Eth -7.3418284 3 NA 3 NA Age NA NA Age -4.3688050 3 NA 7 NA Age:Eth NA NA Age:Eth -4.5213739 3 NA 9 NA Lrn NA NA Lrn -1.4747812 3 NA 2 NA Sex NA NA Sex -0.7363892 3 NA 4 NA Sex:Age NA NA Sex:Age -5.8421931 3 NA 11 NA Age:Lrn NA NA Age:Lrn -2.3115461 3 NA 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 3 NA 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 3 NA 15 NA Age:Eth:Lrn NA NA Age:Eth:Lrn -5.0436262 3 0.05589953 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 3 NA 12 NA Sex:Age:Lrn NA NA Sex:Age:Lrn -3.4094829 3 0.05778817 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 3 0.02479174 grouping term block score Iteration LRT 1 NA 1 NA NA 1 NA 4 NA 5 NA Eth NA NA Eth -7.3418284 4 NA 3 NA Age NA NA Age -4.3688050 4 NA 7 NA Age:Eth NA NA Age:Eth -4.5213739 4 NA 9 NA Lrn NA NA Lrn -1.4747812 4 NA 2 NA Sex NA NA Sex -0.7363892 4 NA 4 NA Sex:Age NA NA Sex:Age -5.8421931 4 0.0001968215 11 NA Age:Lrn NA NA Age:Lrn -2.3115461 4 NA 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 4 NA 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 4 NA 15 NA Age:Eth:Lrn NA NA Age:Eth:Lrn -5.0436262 4 0.1153201660 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 4 NA 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 4 0.0191462752 grouping term block score Iteration LRT 1 NA 1 NA NA 1 NA 5 NA 5 NA Eth NA NA Eth -7.3418284 5 NA 3 NA Age NA NA Age -4.3688050 5 NA 7 NA Age:Eth NA NA Age:Eth -4.5213739 5 1.453244e-01 9 NA Lrn NA NA Lrn -1.4747812 5 NA 2 NA Sex NA NA Sex -0.7363892 5 NA 4 NA Sex:Age NA NA Sex:Age -5.8421931 5 9.829745e-05 11 NA Age:Lrn NA NA Age:Lrn -2.3115461 5 1.504820e-01 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 5 NA 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 5 NA 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 5 NA 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 5 2.534679e-03 grouping term block score Iteration LRT 1 NA 1 NA NA 1 NA 6 NA 5 NA Eth NA NA Eth -7.3418284 6 NA 3 NA Age NA NA Age -4.3688050 6 NA 7 NA Age:Eth NA NA Age:Eth -4.5213739 6 0.1214196689 9 NA Lrn NA NA Lrn -1.4747812 6 NA 2 NA Sex NA NA Sex -0.7363892 6 NA 4 NA Sex:Age NA NA Sex:Age -5.8421931 6 0.0003568777 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 6 NA 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 6 NA 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 6 NA 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 6 0.0036727027 grouping term block score Iteration LRT 1 NA 1 NA NA 1 NA 7 NA 5 NA Eth NA NA Eth -7.3418284 7 NA 3 NA Age NA NA Age -4.3688050 7 NA 9 NA Lrn NA NA Lrn -1.4747812 7 NA 2 NA Sex NA NA Sex -0.7363892 7 NA 4 NA Sex:Age NA NA Sex:Age -5.8421931 7 0.0003276936 6 NA Sex:Eth NA NA Sex:Eth -1.4839163 7 NA 13 NA Eth:Lrn NA NA Eth:Lrn -0.8697238 7 NA 10 NA Sex:Lrn NA NA Sex:Lrn -0.2816163 7 NA 14 NA Sex:Eth:Lrn NA NA Sex:Eth:Lrn -2.2336293 7 0.0004243969 [ FAIL 1 | WARN 6 | SKIP 17 | PASS 15 ] â•â• Skipped tests (17) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• • On CRAN (17): 'test-buildGLMMadaptive.R:4:2', 'test-buildGLMMadaptive.R:10:2', 'test-buildbam.R:4:2', 'test-buildclmm.R:4:2', 'test-buildcustom.R:4:2', 'test-buildgam.R:4:2', 'test-buildgamm.R:4:2', 'test-buildgamm4.R:4:2', 'test-buildglmmTMB.R:4:2', 'test-buildgls.R:4:2', 'test-buildlme.R:4:2', 'test-buildmer-package.R:4:2', 'test-buildmertree.R:4:2', 'test-buildmultinom.R:4:2', 'test-converged.R:4:2', 'test-diag-formula.method.R:11:2', 'test-re2mgcv.R:6:2' â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Error ('test-include.R:4:2'): include ─────────────────────────────────────── Error in `reduce.model(p, conv)`: No terms left for reduction, giving up Backtrace: â–† 1. └─buildmer::buildmer(...) at test-include.R:4:9 2. └─buildmer:::buildmer.fit(p) 3. ├─base::do.call(...) 4. └─buildmer:::order(p = `<named list>`) 5. └─buildmer (local) reorder(p, tab[fxd, ]) 6. └─buildmer:::reduce.model(p, conv) [ FAIL 1 | WARN 6 | SKIP 17 | PASS 15 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [62s/80s] 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: 2 ERRORs