CRAN Package Check Results for Package glmmTMB

Last updated on 2023-04-01 04:56:18 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.6 260.84 318.78 579.62 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.6 219.50 247.87 467.37 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.6 778.73 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.6 810.56 ERROR
r-devel-windows-x86_64 1.1.6 285.00 0.00 285.00 ERROR --no-vignettes
r-patched-linux-x86_64 1.1.6 229.71 310.11 539.82 ERROR
r-release-linux-x86_64 1.1.6 202.68 304.96 507.64 OK
r-release-macos-arm64 1.1.6 153.00 NOTE
r-release-macos-x86_64 1.1.6 242.00 NOTE
r-release-windows-x86_64 1.1.6 313.00 347.00 660.00 NOTE --no-vignettes
r-oldrel-macos-arm64 1.1.6 190.00 NOTE
r-oldrel-macos-x86_64 1.1.6 256.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1.6 575.00 465.00 1040.00 NOTE --no-vignettes

Check Details

Version: 1.1.6
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [93s/112s]
    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) (2023-03-29 r84123)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Debian GNU/Linux 12 (bookworm)
    
     Matrix products: default
     BLAS: /home/hornik/tmp/R.check/r-devel-clang/Work/build/lib/libRblas.so
     LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
    
     locale:
     [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
     [4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
     [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
     [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
    
     time zone: Europe/Vienna
     tzcode source: system (glibc)
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.6 testthat_3.1.7
    
     loaded via a namespace (and not attached):
     [1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
     [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
     [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.3
     [10] lme4_1.1-32 brio_1.1.3 grid_4.4.0
     [13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
     [16] compiler_4.4.0 multcomp_1.4-23 codetools_0.2-19
     [19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
     [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
     [25] R6_2.5.1 splines_4.4.0 magrittr_2.0.3
     [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S12..3.S
     trickier examples: SS.SSSS......
     bootMer:
     bootMer: SS
     checkRank: ..................................W......W..
     control: SS
     diagnose: .S
     disp: ...
     downstream: S..
     edgecases:
     test edge cases: .
     env:
     basic examples: ...
     families:
     alternative binomial specifications: ..........
     non-integer count warnings: .......
     fitting exotic families: SSSSS
     trunc compois: S
     compois: S
     genpois: S
     tweedie: S.
     link function info available: ............
     link info added to family: ......
     formulas:
     formula parsing: ................
     mapopt:
     methods: ............................S....................................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S.............
     misc: .
     offset: SSSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
     reml:
     REML: .......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .......
     start: ..
     utils: ..............
     varstruc:
     variance structures: ........SSS.
     weight: .........
     zi:
     ZI models: SS
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
    
     2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
    
     3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
    
     4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
    
     5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
    
     6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
    
     7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
    
     8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
    
     9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
    
     10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
    
     11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
    
     18. beta ('test-families.R:90:3') - Reason: On CRAN
    
     19. nbinom ('test-families.R:112:5') - Reason: On CRAN
    
     20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
    
     21. truncated ('test-families.R:240:5') - Reason: On CRAN
    
     22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
    
     23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
    
     24. compois ('test-families.R:345:5') - Reason: On CRAN
    
     25. genpois ('test-families.R:356:5') - Reason: On CRAN
    
     26. tweedie ('test-families.R:365:5') - Reason: On CRAN
    
     27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
    
     28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
    
     29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
    
     30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
    
     32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
    
     34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
    
     35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
    
     36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
    
     37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
    
     38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
    
     39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
    
     40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
    
     41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
    
     42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
    
     43. scale ('test-predict.R:183:5') - Reason: On CRAN
    
     44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
    
     45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
    
     46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
    
     47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
    
     48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
    
     49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
    
     50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
    
     51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
    
     52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
    
     53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
    
     54. zi ('test-zi.R:12:3') - Reason: On CRAN
    
     55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
    
     ══ Warnings ════════════════════════════════════════════════════════════════════
     1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
     `gm0` not equal to `res_chr`.
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
     `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.6
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [75s/115s]
    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) (2023-03-29 r84123)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Debian GNU/Linux 12 (bookworm)
    
     Matrix products: default
     BLAS: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libRblas.so
     LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
    
     locale:
     [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
     [4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
     [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
     [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
    
     time zone: Europe/Vienna
     tzcode source: system (glibc)
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.6 testthat_3.1.7
    
     loaded via a namespace (and not attached):
     [1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
     [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
     [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.3
     [10] lme4_1.1-32 brio_1.1.3 grid_4.4.0
     [13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
     [16] compiler_4.4.0 multcomp_1.4-23 codetools_0.2-19
     [19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
     [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
     [25] R6_2.5.1 splines_4.4.0 magrittr_2.0.3
     [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S12..3.S
     trickier examples: SS.SSSS......
     bootMer:
     bootMer: SS
     checkRank: ..................................W......W..
     control: SS
     diagnose: .S
     disp: ...
     downstream: S..
     edgecases:
     test edge cases: .
     env:
     basic examples: ...
     families:
     alternative binomial specifications: ..........
     non-integer count warnings: .......
     fitting exotic families: SSSSS
     trunc compois: S
     compois: S
     genpois: S
     tweedie: S.
     link function info available: ............
     link info added to family: ......
     formulas:
     formula parsing: ................
     mapopt:
     methods: ............................S....................................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S.............
     misc: .
     offset: SSSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
     reml:
     REML: .......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .......
     start: ..
     utils: ..............
     varstruc:
     variance structures: ........SSS.
     weight: .........
     zi:
     ZI models: SS
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
    
     2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
    
     3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
    
     4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
    
     5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
    
     6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
    
     7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
    
     8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
    
     9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
    
     10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
    
     11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
    
     18. beta ('test-families.R:90:3') - Reason: On CRAN
    
     19. nbinom ('test-families.R:112:5') - Reason: On CRAN
    
     20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
    
     21. truncated ('test-families.R:240:5') - Reason: On CRAN
    
     22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
    
     23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
    
     24. compois ('test-families.R:345:5') - Reason: On CRAN
    
     25. genpois ('test-families.R:356:5') - Reason: On CRAN
    
     26. tweedie ('test-families.R:365:5') - Reason: On CRAN
    
     27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
    
     28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
    
     29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
    
     30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
    
     32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
    
     34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
    
     35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
    
     36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
    
     37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
    
     38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
    
     39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
    
     40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
    
     41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
    
     42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
    
     43. scale ('test-predict.R:183:5') - Reason: On CRAN
    
     44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
    
     45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
    
     46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
    
     47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
    
     48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
    
     49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
    
     50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
    
     51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
    
     52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
    
     53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
    
     54. zi ('test-zi.R:12:3') - Reason: On CRAN
    
     55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
    
     ══ Warnings ════════════════════════════════════════════════════════════════════
     1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
     `gm0` not equal to `res_chr`.
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
     `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.6
Check: installed package size
Result: NOTE
     installed size is 11.4Mb
     sub-directories of 1Mb or more:
     doc 1.3Mb
     libs 6.2Mb
     test_data 2.2Mb
     vignette_data 1.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.1.6
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [118s/479s]
    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) (2023-03-28 r84105)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Fedora Linux 36 (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 3.11.0
    
     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_1.1.6 testthat_3.1.7
    
     loaded via a namespace (and not attached):
     [1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
     [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
     [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.3
     [10] lme4_1.1-32 brio_1.1.3 grid_4.4.0
     [13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
     [16] compiler_4.4.0 multcomp_1.4-23 codetools_0.2-19
     [19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
     [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
     [25] R6_2.5.1 splines_4.4.0 magrittr_2.0.3
     [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S12..3.S
     trickier examples: SS.SSSS......
     bootMer:
     bootMer: SS
     checkRank: ..................................W......W..
     control: SS
     diagnose: .S
     disp: ...
     downstream: S..
     edgecases:
     test edge cases: .
     env:
     basic examples: ...
     families:
     alternative binomial specifications: ..........
     non-integer count warnings: .......
     fitting exotic families: SSSSS
     trunc compois: S
     compois: S
     genpois: S
     tweedie: S.
     link function info available: ............
     link info added to family: ......
     formulas:
     formula parsing: ................
     mapopt:
     methods: ............................S....................................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S.............
     misc: .
     offset: SSSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
     reml:
     REML: .......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .......
     start: ..
     utils: ..............
     varstruc:
     variance structures: ........SSS.
     weight: .........
     zi:
     ZI models: SS
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
    
     2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
    
     3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
    
     4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
    
     5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
    
     6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
    
     7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
    
     8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
    
     9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
    
     10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
    
     11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
    
     18. beta ('test-families.R:90:3') - Reason: On CRAN
    
     19. nbinom ('test-families.R:112:5') - Reason: On CRAN
    
     20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
    
     21. truncated ('test-families.R:240:5') - Reason: On CRAN
    
     22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
    
     23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
    
     24. compois ('test-families.R:345:5') - Reason: On CRAN
    
     25. genpois ('test-families.R:356:5') - Reason: On CRAN
    
     26. tweedie ('test-families.R:365:5') - Reason: On CRAN
    
     27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
    
     28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
    
     29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
    
     30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
    
     32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
    
     34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
    
     35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
    
     36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
    
     37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
    
     38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
    
     39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
    
     40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
    
     41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
    
     42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
    
     43. scale ('test-predict.R:183:5') - Reason: On CRAN
    
     44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
    
     45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
    
     46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
    
     47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
    
     48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
    
     49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
    
     50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
    
     51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
    
     52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
    
     53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
    
     54. zi ('test-zi.R:12:3') - Reason: On CRAN
    
     55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
    
     ══ Warnings ════════════════════════════════════════════════════════════════════
     1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
     `gm0` not equal to `res_chr`.
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
     `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.6
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [113s/406s]
    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) (2023-03-28 r84105)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Fedora Linux 36 (Workstation Edition)
    
     Matrix products: default
     BLAS: /data/gannet/ripley/R/R-devel/lib/libRblas.so
     LAPACK: /usr/lib64/liblapack.so.3.10.1
    
     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_1.1.6 testthat_3.1.7
    
     loaded via a namespace (and not attached):
     [1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
     [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
     [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.3
     [10] lme4_1.1-32 brio_1.1.3 grid_4.4.0
     [13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
     [16] compiler_4.4.0 multcomp_1.4-23 codetools_0.2-19
     [19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
     [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
     [25] R6_2.5.1 splines_4.4.0 magrittr_2.0.3
     [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S12..3.S
     trickier examples: SS.SSSS......
     bootMer:
     bootMer: SS
     checkRank: ..................................W......W..
     control: SS
     diagnose: .S
     disp: ...
     downstream: S..
     edgecases:
     test edge cases: .
     env:
     basic examples: ...
     families:
     alternative binomial specifications: ..........
     non-integer count warnings: .......
     fitting exotic families: SSSSS
     trunc compois: S
     compois: S
     genpois: S
     tweedie: S.
     link function info available: ............
     link info added to family: ......
     formulas:
     formula parsing: ................
     mapopt:
     methods: ............................S....................................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S.............
     misc: .
     offset: SSSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
     reml:
     REML: .......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .......
     start: ..
     utils: ..............
     varstruc:
     variance structures: ........SSS.
     weight: .........
     zi:
     ZI models: SS
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
    
     2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
    
     3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
    
     4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
    
     5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
    
     6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
    
     7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
    
     8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
    
     9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
    
     10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
    
     11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
    
     18. beta ('test-families.R:90:3') - Reason: On CRAN
    
     19. nbinom ('test-families.R:112:5') - Reason: On CRAN
    
     20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
    
     21. truncated ('test-families.R:240:5') - Reason: On CRAN
    
     22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
    
     23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
    
     24. compois ('test-families.R:345:5') - Reason: On CRAN
    
     25. genpois ('test-families.R:356:5') - Reason: On CRAN
    
     26. tweedie ('test-families.R:365:5') - Reason: On CRAN
    
     27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
    
     28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
    
     29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
    
     30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
    
     32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
    
     34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
    
     35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
    
     36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
    
     37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
    
     38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
    
     39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
    
     40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
    
     41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
    
     42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
    
     43. scale ('test-predict.R:183:5') - Reason: On CRAN
    
     44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
    
     45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
    
     46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
    
     47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
    
     48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
    
     49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
    
     50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
    
     51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
    
     52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
    
     53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
    
     54. zi ('test-zi.R:12:3') - Reason: On CRAN
    
     55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
    
     ══ Warnings ════════════════════════════════════════════════════════════════════
     1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
     `gm0` not equal to `res_chr`.
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
     `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.6
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 9.4Mb
     sub-directories of 1Mb or more:
     doc 1.3Mb
     libs 4.3Mb
     test_data 2.2Mb
     vignette_data 1.1Mb
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.6
Flags: --no-vignettes
Check: tests
Result: ERROR
     Running 'AAAtest-all.R' [72s]
    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 version 4.3.0 alpha (2023-03-26 r84066 ucrt)
     Platform: x86_64-w64-mingw32/x64 (64-bit)
     Running under: Windows Server 2022 x64 (build 20348)
    
     Matrix products: default
    
    
     locale:
     [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8
     [3] LC_MONETARY=C LC_NUMERIC=C
     [5] LC_TIME=C
    
     time zone: Europe/Berlin
     tzcode source: internal
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.6 testthat_3.1.7
    
     loaded via a namespace (and not attached):
     [1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
     [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
     [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2
     [10] lme4_1.1-32 brio_1.1.3 grid_4.3.0
     [13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
     [16] compiler_4.3.0 multcomp_1.4-23 codetools_0.2-19
     [19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
     [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
     [25] R6_2.5.1 splines_4.3.0 magrittr_2.0.3
     [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S12..3.S
     trickier examples: SS.SSSS......
     bootMer:
     bootMer: SS
     checkRank: ..................................W......W..
     control: SS
     diagnose: .S
     disp: ...
     downstream: S..
     edgecases:
     test edge cases: .
     env:
     basic examples: ...
     families:
     alternative binomial specifications: ..........
     non-integer count warnings: .......
     fitting exotic families: SSSSS
     trunc compois: S
     compois: S
     genpois: S
     tweedie: S.
     link function info available: ............
     link info added to family: ......
     formulas:
     formula parsing: ................
     mapopt:
     methods: ............................S....................................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S.............
     misc: .
     offset: SSSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSS...S..S...S.............S.W...
     reml:
     REML: .......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .......
     start: ..
     utils: ..............
     varstruc:
     variance structures: ........SSS.
     weight: .........
     zi:
     ZI models: SS
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
    
     2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
    
     3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
    
     4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
    
     5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
    
     6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
    
     7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
    
     8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
    
     9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
    
     10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
    
     11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
    
     18. beta ('test-families.R:90:3') - Reason: On CRAN
    
     19. nbinom ('test-families.R:112:5') - Reason: On CRAN
    
     20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
    
     21. truncated ('test-families.R:240:5') - Reason: On CRAN
    
     22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
    
     23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
    
     24. compois ('test-families.R:345:5') - Reason: On CRAN
    
     25. genpois ('test-families.R:356:5') - Reason: On CRAN
    
     26. tweedie ('test-families.R:365:5') - Reason: On CRAN
    
     27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
    
     28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
    
     29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
    
     30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
    
     32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
    
     34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
    
     35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
    
     36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
    
     37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
    
     38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
    
     39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
    
     40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
    
     41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
    
     42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
    
     43. scale ('test-predict.R:183:5') - Reason: On CRAN
    
     44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
    
     45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
    
     46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
    
     47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
    
     48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
    
     49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
    
     50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
    
     51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
    
     52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
    
     53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
    
     54. zi ('test-zi.R:12:3') - Reason: On CRAN
    
     55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
    
     ══ Warnings ════════════════════════════════════════════════════════════════════
     1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
     `gm0` not equal to `res_chr`.
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
     `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 1.1.6
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [90s/104s]
    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 version 4.3.0 alpha (2023-03-27 r84084)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Debian GNU/Linux 12 (bookworm)
    
     Matrix products: default
     BLAS: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib/libRblas.so
     LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
    
     locale:
     [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
     [4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
     [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
     [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
    
     time zone: Europe/Vienna
     tzcode source: system (glibc)
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.6 testthat_3.1.7
    
     loaded via a namespace (and not attached):
     [1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
     [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
     [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2
     [10] lme4_1.1-32 brio_1.1.3 grid_4.3.0
     [13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
     [16] compiler_4.3.0 multcomp_1.4-23 codetools_0.2-19
     [19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
     [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
     [25] R6_2.5.1 splines_4.3.0 magrittr_2.0.3
     [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S12..3.S
     trickier examples: SS.SSSS......
     bootMer:
     bootMer: SS
     checkRank: ..................................W......W..
     control: SS
     diagnose: .S
     disp: ...
     downstream: S..
     edgecases:
     test edge cases: .
     env:
     basic examples: ...
     families:
     alternative binomial specifications: ..........
     non-integer count warnings: .......
     fitting exotic families: SSSSS
     trunc compois: S
     compois: S
     genpois: S
     tweedie: S.
     link function info available: ............
     link info added to family: ......
     formulas:
     formula parsing: ................
     mapopt:
     methods: ............................S....................................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S.............
     misc: .
     offset: SSSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
     reml:
     REML: .......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .......
     start: ..
     utils: ..............
     varstruc:
     variance structures: ........SSS.
     weight: .........
     zi:
     ZI models: SS
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
    
     2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
    
     3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
    
     4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
    
     5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
    
     6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
    
     7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
    
     8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
    
     9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
    
     10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
    
     11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
    
     18. beta ('test-families.R:90:3') - Reason: On CRAN
    
     19. nbinom ('test-families.R:112:5') - Reason: On CRAN
    
     20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
    
     21. truncated ('test-families.R:240:5') - Reason: On CRAN
    
     22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
    
     23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
    
     24. compois ('test-families.R:345:5') - Reason: On CRAN
    
     25. genpois ('test-families.R:356:5') - Reason: On CRAN
    
     26. tweedie ('test-families.R:365:5') - Reason: On CRAN
    
     27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
    
     28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
    
     29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
    
     30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
    
     32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
    
     34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
    
     35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
    
     36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
    
     37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
    
     38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
    
     39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
    
     40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
    
     41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
    
     42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
    
     43. scale ('test-predict.R:183:5') - Reason: On CRAN
    
     44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
    
     45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
    
     46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
    
     47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
    
     48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
    
     49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
    
     50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
    
     51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
    
     52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
    
     53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
    
     54. zi ('test-zi.R:12:3') - Reason: On CRAN
    
     55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
    
     ══ Warnings ════════════════════════════════════════════════════════════════════
     1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
     `gm0` not equal to `res_chr`.
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
     `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
     Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-patched-linux-x86_64