Source: r-cran-glmmtmb
Version: 1.1.5+dfsg-4
Severity: serious
Justification: autopkgtest failure
Dear Maintainer,
The autopkgtest of your package fails with r-base (4.3.1-1):
50s autopkgtest [01:19:09]: test run-unit-test: [-----------------------
50s dpkg-architecture: warning: cannot determine CC system type, falling back
to default (native compilation)
50s BEGIN TEST AAAtest-all.R
50s
50s R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
50s Copyright (C) 2023 The R Foundation for Statistical Computing
50s Platform: x86_64-pc-linux-gnu (64-bit)
50s
50s R is free software and comes with ABSOLUTELY NO WARRANTY.
50s You are welcome to redistribute it under certain conditions.
50s Type 'license()' or 'licence()' for distribution details.
50s
50s R is a collaborative project with many contributors.
50s Type 'contributors()' for more information and
50s 'citation()' on how to cite R or R packages in publications.
50s
50s Type 'demo()' for some demos, 'help()' for on-line help, or
50s 'help.start()' for an HTML browser interface to help.
50s Type 'q()' to quit R.
50s
50s > if (require("testthat")) {
50s + pkg <- "glmmTMB"
50s + require(pkg, character.only=TRUE)
50s + print(sessionInfo())
50s + test_check(pkg, reporter="summary")
50s + print(warnings()) # TODO? catch most of these by expect_warning(..)
50s + } else {
50s + warnings("Package 'testthat' not available, cannot run unit tests
for package",
50s + sQuote(pkg))
50s + }
50s Loading required package: testthat
51s Loading required package: glmmTMB
52s R version 4.3.1 (2023-06-16)
52s Platform: x86_64-pc-linux-gnu (64-bit)
52s Running under: Debian GNU/Linux trixie/sid
52s
52s Matrix products: default
52s BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
52s LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
52s
52s locale:
52s [1] C
52s
52s time zone: Etc/UTC
52s tzcode source: system (glibc)
52s
52s attached base packages:
52s [1] stats graphics grDevices utils datasets methods base
52s
52s other attached packages:
52s [1] glmmTMB_1.1.5 testthat_3.1.6
52s
52s loaded via a namespace (and not attached):
52s [1] nlme_3.1-162 cli_3.6.0 rlang_1.0.6
52s [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
52s [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2
52s [10] lme4_1.1-31 brio_1.1.3 grid_4.3.1
52s [13] MASS_7.3-60 mvtnorm_1.1-3 numDeriv_2016.8-1.1
52s [16] compiler_4.3.1 multcomp_1.4-22 codetools_0.2-19
52s [19] sandwich_3.0-2 emmeans_1.8.4-1 coda_0.19-4
52s [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
52s [25] R6_2.5.1 splines_4.3.1 magrittr_2.0.3
52s [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-3
53s Anova: ..............
56s VarCorr: .............
56s altopt:
56s alternative optimizers: S
58s basics: .............SS.....S12..3.S
59s trickier examples: SS.SSSS......
59s bootMer:
59s bootMer: SS
65s checkRank: ..................................W......W..
65s control: SS
65s diagnose: .
67s disp: ...
68s downstream: S..
68s edgecases:
68s test edge cases: .
68s env:
70s basic examples: ...
70s families:
71s alternative binomial specifications: ..........
73s non-integer count warnings: .......
73s fitting exotic families: SSSSS
73s trunc compois: S
73s compois: S
73s genpois: S
73s tweedie: S.
73s link function info available: ............
74s link info added to family: ......
74s formulas:
74s formula parsing: ................
74s mapopt:
79s methods:
............................S....................................................
79s simulate consistency with glm/lm: ...
82s Ranef etc.: .......S...........
83s misc: .
83s offset: SSSSSSSSS
83s predict: .....SSS
88s Predict two-column response case:
SS.................S..SSS...S..S...S.............S.W.W..
88s reml:
89s REML: .......
89s rr: W
89s saveload:
90s Saving and loading glmmTMB objects: .
90s sparseX:
90s sparse X models: .......
90s start: ..
90s utils: ..............
90s varstruc:
90s variance structures: ........SSS
91s weight: .........
91s zi:
91s ZI models: SS
91s
91s == Skipped
=====================================================================
91s 1. downstream methods work with optim() ('test-altopt.R:11') - Reason: On
CRAN
91s
91s 2. Update Gaussian ('test-basics.R:68') - Reason: On CRAN
91s
91s 3. Variance structures ('test-basics.R:77') - Reason: On CRAN
91s
91s 4. Multiple RE, reordering ('test-basics.R:107') - Reason: On CRAN
91s
91s 5. close to lme4 results ('test-basics.R:142') - Reason: On CRAN
91s
91s 6. basic zero inflation ('test-basics.R:195') - Reason: On CRAN
91s
91s 7. alternative binomial model specifications ('test-basics.R:213') -
Reason: On CRAN
91s
91s 8. NA handling ('test-basics.R:234') - Reason: On CRAN
91s
91s 9. quine NB fit ('test-basics.R:252') - Reason: On CRAN
91s
91s 10. contrasts arg ('test-basics.R:263') - Reason: On CRAN
91s
91s 11. zero disp setting ('test-basics.R:274') - Reason: On CRAN
91s
91s 12. Bernoulli responses ('test-bootMer.R:12') - Reason: On CRAN
91s
91s 13. binomial responses ('test-bootMer.R:22') - Reason: On CRAN
91s
91s 14. profile method ('test-control.R:16') - Reason: On CRAN
91s
91s 15. parallel regions ('test-control.R:50') - Reason: On CRAN
91s
91s 16. emmeans ('test-downstream.R:8') - Reason: On CRAN
91s
91s 17. beta ('test-families.R:90') - Reason: On CRAN
91s
91s 18. nbinom ('test-families.R:112') - Reason: On CRAN
91s
91s 19. dbetabinom ('test-families.R:167') - Reason: On CRAN
91s
91s 20. truncated ('test-families.R:240') - Reason: On CRAN
91s
91s 21. truncated_genpois ('test-families.R:317') - Reason: On CRAN
91s
91s 22. truncated_compois ('test-families.R:334') - Reason: On CRAN
91s
91s 23. compois ('test-families.R:345') - Reason: On CRAN
91s
91s 24. genpois ('test-families.R:356') - Reason: On CRAN
91s
91s 25. tweedie ('test-families.R:365') - Reason: On CRAN
91s
91s 26. anova ML/REML checks ('test-methods.R:117') - Reason: On CRAN
91s
91s 27. various binomial response types work ('test-methods.R:478') - Reason:
On CRAN
91s
91s 28. LM with offset as argument ('test-offset.R:27') - Reason: On CRAN
91s
91s 29. LM with offset in formula ('test-offset.R:35') - Reason: On CRAN
91s
91s 30. LM with offset in formula - variable not in environment
('test-offset.R:48') - Reason: On CRAN
91s
91s 31. LM with offset in dispersion formula ('test-offset.R:57') - Reason: On
CRAN
91s
91s 32. LM with multiple offsets (cond/dispersion) ('test-offset.R:65') -
Reason: On CRAN
91s
91s 33. LM with random crap in the formula ('test-offset.R:74') - Reason: On
CRAN
91s
91s 34. offset in do.call ('test-offset.R:81') - Reason: On CRAN
91s
91s 35. LONG offset in do.call ('test-offset.R:90') - Reason: On CRAN
91s
91s 36. offset works with attributes ('test-offset.R:101') - Reason: On CRAN
91s
91s 37. new levels of fixed effect factor ('test-predict.R:37') - Reason: On
CRAN
91s
91s 38. new levels in RE term ('test-predict.R:44') - Reason: On CRAN
91s
91s 39. new levels in AR1 (OK) ('test-predict.R:51') - Reason: On CRAN
91s
91s 40. two-column response ('test-predict.R:61') - Reason: On CRAN
91s
91s 41. Prediction with dispformula=~0 ('test-predict.R:69') - Reason: On CRAN
91s
91s 42. scale ('test-predict.R:183') - Reason: On CRAN
91s
91s 43. scale_RE ('test-predict.R:205') - Reason: On CRAN
91s
91s 44. complex bases in dispformula ('test-predict.R:212') - Reason: On CRAN
91s
91s 45. fix_predvars works for I(x^2) ('test-predict.R:224') - Reason: On CRAN
91s
91s 46. contrasts carried over ('test-predict.R:285') - Reason: On CRAN
91s
91s 47. offset-only model (GH #625) ('test-predict.R:324') - Reason: On CRAN
91s
91s 48. inverse-link prediction ('test-predict.R:343') - Reason: On CRAN
91s
91s 49. nzprob doesn't segfault ('test-predict.R:434') - Reason: On CRAN
91s
91s 50. ar1 requires factor time ('test-varstruc.R:52') - Reason: On CRAN
91s
91s 51. varcorr_print ('test-varstruc.R:72') - Reason: On CRAN
91s
91s 52. cov_struct_order ('test-varstruc.R:103') - Reason: On CRAN
91s
91s 53. zi ('test-zi.R:12') - Reason: On CRAN
91s
91s 54. zi beta and Gamma ('test-zi.R:37') - Reason: On CRAN
91s
91s == Warnings
====================================================================
91s 1. equivalence between 'skip' and 'warn' when confronted with identifiable
and non-identifiable fixed effects ('test-checkRank.R:138') - Model convergence
problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
91s
91s 2. equivalence between 'skip' and 'warn' when confronted with identifiable
and non-identifiable fixed effects ('test-checkRank.R:157') - Model convergence
problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
91s
91s 3. nzprob computed for non-fast pred (???) - Model convergence problem;
non-positive-definite Hessian matrix. See vignette('troubleshooting')
91s
91s 4. nzprob computed for non-fast pred (???) - Model convergence problem;
non-positive-definite Hessian matrix. See vignette('troubleshooting')
91s
91s 5. (code run outside of `test_that()`) ('test-rr.R:9') - there is no
package called 'mvabund'
91s
91s == Failed
======================================================================
91s -- 1. Failure ('test-basics.R:120'): Alternative family specifications
[via upda
91s `gm0` not equal to `res_chr`.
91s Component "modelInfo": Component "family": Length mismatch: comparison on
first 12 components
91s
91s -- 2. Failure ('test-basics.R:121'): Alternative family specifications
[via upda
91s `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn =
TRUE).
91s Component "modelInfo": Component "family": Length mismatch: comparison on
first 12 components
91s
91s -- 3. Failure ('test-basics.R:132'): Update Binomial
---------------------------
91s `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
91s Component "modelInfo": Component "family": Length mismatch: comparison on
first 12 components
91s
91s == DONE
========================================================================
91s Error: Test failures
https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-glmmtmb/34918480/log.gz
