* 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 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • 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'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── 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