* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/glmmTMB.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘glmmTMB/DESCRIPTION’ ... OK
* this is package ‘glmmTMB’ version ‘1.1.10’
* 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 ‘glmmTMB’ can be installed ... [9m/11m] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/glmmTMB-00install.html' for details.
* used C++ compiler: ‘clang version 20.1.0-rc3’
* checking installed package size ... INFO
installed size is 12.9Mb
sub-directories of 1Mb or more:
doc 1.3Mb
libs 6.3Mb
test_data 2.3Mb
vignette_data 2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘methods.R’
* 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 ... [45s/55s] 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/28s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [150s/190s] ERROR
Running ‘AAAtest-all.R’ [150s/190s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Complete output:
> if (require("testthat")) {
+ pkg <- "glmmTMB"
+ require(pkg, character.only=TRUE)
+ print(sessionInfo())
+ test_check(pkg, reporter="summary")
+ print(warnings()) # TODO? catch most of these by expect_warning(..)
+ } else {
+ warnings("Package 'testthat' not available, cannot run unit tests for package",
+ sQuote(pkg))
+ }
Loading required package: testthat
Loading required package: glmmTMB
R Under development (unstable) (2025-02-28 r87848)
Platform: x86_64-pc-linux-gnu
Running under: Fedora Linux 40 (Workstation Edition)
Matrix products: default
BLAS: /data/gannet/ripley/R/R-clang/lib/libRblas.so
LAPACK: /data/gannet/ripley/R/R-clang/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmmTMB_1.1.10 testthat_3.2.3
loaded via a namespace (and not attached):
[1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3
[4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0
[7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13
[10] TMB_1.9.16 lme4_1.1-36 brio_1.1.5
[13] grid_4.5.0 MASS_7.3-65 mvtnorm_1.3-3
[16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.5.0
[19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.10.7
[22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1
[25] lattice_0.22-6 nloptr_2.1.1 R6_2.6.1
[28] Rdpack_2.6.2 splines_4.5.0 rbibutils_2.3
[31] magrittr_2.0.3 Matrix_1.7-2 tools_4.5.0
[34] boot_1.3-31 survival_3.8-3
Anova: WW12.............
VarCorr: WWW3.4.WWW...........
altopt:
alternative optimizers: S
basics: .............SS.....S......S
trickier examples: SS.SSSS........
bootMer:
bootMer: SS
checkRank: ................................................
control: SS.
diagnose: .S
disp: ...
downstream: S.....
edgecases:
test edge cases: .
env:
basic examples: ...
families: .....................SSSSSSSSS..................................
formulas:
formula parsing: ................
mapequal: ........
mapopt:
methods: ...............................S..........................................S..............S.......................
misc: .
offset: SSSSSSSSS
predict: .....SSS
Predict two-column response case: SS.................S..SSS..WWW.5S..S...S.............S.......
priors: ...........S
propto: .....
reml: WWW678WWW9ab..
rr: .........
saveload:
Saving and loading glmmTMB objects: .
simulate: .........
simulate_new: ....S.........
smooths: ......
sparseX:
sparse X models: .......
start: ..
utils: .........................................................................................................
varstruc:
variance structures: ........SSS.
weight: .........
zi:
ZI models: SS
â•â• Skipped 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•â•â•â•â•â•
1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
2. Update Gaussian ('test-basics.R:85:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:94:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:124:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:164:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:217:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:236:5') - Reason: On CRAN
8. NA handling ('test-basics.R:257:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:275:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:286:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:297:5') - Reason: On CRAN
12. Bernoulli responses ('test-bootMer.R:12:3') - Reason: On CRAN
13. binomial responses ('test-bootMer.R:22:5') - Reason: On CRAN
14. profile method ('test-control.R:16:3') - Reason: On CRAN
15. parallel regions ('test-control.R:50:3') - Reason: On CRAN
16. diagnose works with Tweedie fits ('test-diagnose.R:16:5') - Reason: On CRAN
17. emmeans ('test-downstream.R:22:5') - Reason: On CRAN
18. beta ('test-families.R:103:3') - Reason: On CRAN
19. nbinom ('test-families.R:125:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:186:5') - Reason: On CRAN
21. truncated ('test-families.R:259:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:336:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:352:5') - Reason: On CRAN
24. compois ('test-families.R:362:5') - Reason: On CRAN
25. genpois ('test-families.R:372:5') - Reason: On CRAN
26. tweedie ('test-families.R:380:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN
28. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test
29. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN
30. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
31. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
32. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
33. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
34. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
35. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
36. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
37. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
38. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
39. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
40. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
41. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
42. two-column response ('test-predict.R:61:5') - Reason: On CRAN
43. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
44. scale ('test-predict.R:183:5') - Reason: On CRAN
45. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
46. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
47. fix_predvars works for I(x^2) ('test-predict.R:225:5') - Reason: On CRAN
48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN
49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN
50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN
51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN
52. prior specs ('test-priors.R:125:5') - Reason: On CRAN
53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test
54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN
55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN
56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN
57. zi ('test-zi.R:12:3') - Reason: On CRAN
58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
â•â• Warnings 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•â•â•â•â•
1. basic car::Anova ('test-Anova.R:27:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
2. basic car::Anova ('test-Anova.R:27:5') - Model failed to converge with max|grad| = 1.84934 (tol = 0.002, component 1)
3. (code run outside of `test_that()`) ('test-VarCorr.R:9:1') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
4. (code run outside of `test_that()`) ('test-VarCorr.R:9:1') - unable to evaluate scaled gradient
5. (code run outside of `test_that()`) ('test-VarCorr.R:9:1') - Model failed to converge: degenerate Hessian with 2 negative eigenvalues
6. (code run outside of `test_that()`) ('test-VarCorr.R:53:1') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
7. (code run outside of `test_that()`) ('test-VarCorr.R:53:1') - unable to evaluate scaled gradient
8. (code run outside of `test_that()`) ('test-VarCorr.R:53:1') - Model failed to converge: degenerate Hessian with 2 negative eigenvalues
9. predvars with differing splines in fixed and RE (GH#632) ('test-predict.R:279:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
10. predvars with differing splines in fixed and RE (GH#632) ('test-predict.R:279:5') - unable to evaluate scaled gradient
11. predvars with differing splines in fixed and RE (GH#632) ('test-predict.R:279:5') - Model failed to converge: degenerate Hessian with 1 negative eigenvalues
12. REML check against lmer ('test-reml.R:11:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
13. REML check against lmer ('test-reml.R:11:5') - unable to evaluate scaled gradient
14. REML check against lmer ('test-reml.R:11:5') - Model failed to converge: degenerate Hessian with 1 negative eigenvalues
15. REML check against lmer ('test-reml.R:22:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
16. REML check against lmer ('test-reml.R:22:5') - unable to evaluate scaled gradient
17. REML check against lmer ('test-reml.R:22:5') - Model failed to converge: degenerate Hessian with 2 negative eigenvalues
â•â• Failed 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•â•â•â•â•â•â•
── 1. Failure ('test-Anova.R:28:5'): basic car::Anova ──────────────────────────
Anova(fm1) not equal to Anova(fm0).
Component "Chisq": Mean relative difference: 0.06009598
── 2. Failure ('test-Anova.R:29:5'): basic car::Anova ──────────────────────────
Anova(fm1, type = "III") not equal to Anova(fm0, type = "III").
Component "Chisq": Mean relative difference: 0.342178
── 3. Failure ('test-VarCorr.R:29:5'): basic glmer vs glmmTMB ──────────────────
stripTMBVC(fm1) not equal to unclass(VarCorr(fm1C)).
Attributes: < Component "sc": Mean relative difference: 0.0960177 >
Component "Subject": Attributes: < Component "correlation": Mean relative difference: 1 >
Component "Subject": Attributes: < Component "stddev": Mean relative difference: 0.8215676 >
Component "Subject": Mean relative difference: 0.9829192
── 4. Failure ('test-VarCorr.R:38:1'): (code run outside of `test_that()`) ─────
tail(pfun(fm1), 4) not equal to pfun(fm1C).
3/4 mismatches
x[2]: "Subject (Intercept) 2.19"
y[2]: "Subject (Intercept) 1.2"
x[3]: "age 0.21 -0.58"
y[3]: "age 1.2 0.00"
x[4]: "Residual 1.31"
y[4]: "Residual 1.2"
── 5. Failure ('test-predict.R:289:5'): predvars with differing splines in fixed
unname(ppB) not equal to `pp`.
3/3 mismatches (average diff: 1.18)
[1] 309 - 309 == -0.512
[2] 320 - 321 == -1.234
[3] 332 - 334 == -1.806
── 6. Failure ('test-reml.R:13:5'): REML check against lmer ────────────────────
logLik(fm1.lmer) not equal to logLik(fm1.glmmTMB).
Mean absolute difference: Inf
── 7. Failure ('test-reml.R:14:5'): REML check against lmer ────────────────────
as.vector(predict(fm1.lmer)) not equal to predict(fm1.glmmTMB).
179/180 mismatches (average diff: 1.93)
[1] 246 - 254 == -7.177
[2] 268 - 273 == -5.479
[3] 289 - 293 == -3.781
[4] 311 - 313 == -2.083
[5] 332 - 332 == -0.385
[6] 353 - 352 == 1.313
[7] 375 - 372 == 3.011
[8] 396 - 391 == 4.709
[9] 417 - 411 == 6.407
...
── 8. Failure ('test-reml.R:16:5'): REML check against lmer ────────────────────
vcov(fm1.glmmTMB)$cond not equal to as.matrix(vcov(fm1.lmer)).
4/4 mismatches (average diff: 8.47)
[1] 46.57 - 44.4 == 2.223
[2] -1.45 - -1.8 == 0.347
[3] -1.45 - -1.8 == 0.347
[4] 2.39 - 33.4 == -30.974
── 9. Failure ('test-reml.R:27:5'): REML check against lmer ────────────────────
logLik(fm2.lmer) not equal to logLik(fm2.glmmTMB).
Mean absolute difference: Inf
── 10. Failure ('test-reml.R:28:5'): REML check against lmer ───────────────────
as.vector(predict(fm2.lmer)) not equal to predict(fm2.glmmTMB).
108/108 mismatches (average diff: 0.161)
[1] 24.8 - 24.8 == -0.03191
[2] 26.8 - 26.6 == 0.17897
[3] 28.7 - 28.3 == 0.38985
[4] 30.7 - 30.1 == 0.60073
[5] 21.5 - 21.4 == 0.06339
[6] 22.8 - 22.8 == 0.00647
[7] 24.1 - 24.1 == -0.05045
[8] 25.4 - 25.5 == -0.10737
[9] 22.2 - 22.2 == 0.02640
...
... and 1 more
Maximum number of 10 failures reached, some test results may be missing.
â•â• DONE 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•â•â•â•â•â•â•â•â•
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [170s/217s] OK
* checking PDF version of manual ... [12s/15s] 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, 1 NOTE