CRAN Package Check Results for Package glmmTMB

Last updated on 2021-07-25 09:50:20 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.2 174.30 304.94 479.24 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.2 161.96 232.75 394.71 OK
r-devel-linux-x86_64-fedora-clang 1.1.2 624.66 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.2 656.93 ERROR
r-devel-windows-x86_64 1.1.2 185.00 226.00 411.00 NOTE --no-vignettes
r-patched-linux-x86_64 1.1.2 168.78 302.44 471.22 ERROR
r-patched-solaris-x86 1.1.2 419.30 ERROR
r-release-linux-x86_64 1.1.2 168.28 295.77 464.05 ERROR
r-release-macos-arm64 1.1.1 NOTE
r-release-macos-x86_64 1.1.2 ERROR
r-oldrel-macos-x86_64 1.1.2 ERROR
r-oldrel-windows-ix86+x86_64 1.1.2 258.00 307.00 565.00 NOTE --no-vignettes

Additional issues

ATLAS gcc11 M1mac MKL noLD OpenBLAS

Check Details

Version: 1.1.2
Check: tests
Result: ERROR
     Running 'AAAtest-all.R' [111s/122s]
    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) (2021-07-22 r80654)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Debian GNU/Linux 11 (bullseye)
    
     Matrix products: default
     BLAS: /home/hornik/tmp/R.check/r-devel-clang/Work/build/lib/libRblas.so
     LAPACK: /home/hornik/tmp/R.check/r-devel-clang/Work/build/lib/libRlapack.so
    
     locale:
     [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
     [3] LC_TIME=en_US.iso885915 LC_COLLATE=C
     [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
     [7] LC_PAPER=en_US.iso885915 LC_NAME=C
     [9] LC_ADDRESS=C LC_TELEPHONE=C
     [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.2.0 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.0 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.2.0
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-11 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.2.0 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Warning: namespace 'GLMMadaptive' is not available and has been replaced
     by .GlobalEnv when processing object 'fit'
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S....1.S
     trickier examples: SS.SSSS
     bootMer:
     bootMer: SS
     control: SS
     disp: ...
     downstream:
     emmeans: .............
     effects: ..
     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:
     basic methods: ...........................S.S....................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S........S.
     offset:
     offsets: SSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSSS..S...S..
     reml:
     REML: ......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .....S
     start: ..
     utils: .............
     varstruc:
     variance structures: ........SSS
     weight:
     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:57:3) - Reason: On CRAN
    
     3. Variance structures (test-basics.R:66:3) - Reason: On CRAN
    
     4. Multiple RE, reordering (test-basics.R:96:6) - Reason: On CRAN
    
     5. close to lme4 results (test-basics.R:131:5) - Reason: On CRAN
    
     6. basic zero inflation (test-basics.R:184:8) - Reason: On CRAN
    
     7. alternative binomial model specifications (test-basics.R:202:5) - Reason: On CRAN
    
     8. NA handling (test-basics.R:223:5) - Reason: On CRAN
    
     9. quine NB fit (test-basics.R:241:5) - Reason: On CRAN
    
     10. contrasts arg (test-basics.R:252:5) - Reason: On CRAN
    
     11. zero disp setting (test-basics.R:263:5) - Reason: On CRAN
    
     12. Bernoulli responses (test-bootMer.R:11:3) - Reason: On CRAN
    
     13. binomial responses (test-bootMer.R:21:5) - 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. beta (test-families.R:88:3) - Reason: On CRAN
    
     17. nbinom (test-families.R:110:5) - Reason: On CRAN
    
     18. dbetabinom (test-families.R:165:5) - Reason: On CRAN
    
     19. truncated (test-families.R:238:5) - Reason: On CRAN
    
     20. truncated_genpois (test-families.R:315:3) - Reason: On CRAN
    
     21. truncated_compois (test-families.R:332:5) - Reason: On CRAN
    
     22. compois (test-families.R:343:5) - Reason: On CRAN
    
     23. genpois (test-families.R:354:5) - Reason: On CRAN
    
     24. tweedie (test-families.R:363:5) - Reason: On CRAN
    
     25. anova ML/REML checks (test-methods.R:114:5) - Reason: On CRAN
    
     26. terms back-compatibility (test-methods.R:157:5) - Reason: skip until TMB fits are back-compatible
    
     27. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
    
     28. trunc nbinom sim 2 (test-methods.R:524:1) - Reason: empty test
    
     29. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
    
     30. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
    
     32. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
    
     34. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
    
     35. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
    
     36. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
    
     37. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
    
     38. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
    
     39. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
    
     40. two-column response (test-predict.R:64:5) - Reason: On CRAN
    
     41. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
    
     42. scale (test-predict.R:186:5) - Reason: On CRAN
    
     43. scale_RE (test-predict.R:208:5) - Reason: On CRAN
    
     44. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
    
     45. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
    
     46. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
    
     47. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
    
     48. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
    
     49. back-compatibility (test-sparseX.R:20:5) - Reason: skip until TMB fits are back-compatible
    
     50. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
    
     51. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
    
     52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
    
     53. zi (test-zi.R:12:3) - Reason: On CRAN
    
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     == Failed ======================================================================
     -- 1. Failure (test-basics.R:121:3): Update Binomial ---------------------------
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 2.131994e-08
    
     == DONE ========================================================================
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.2
Check: installed package size
Result: NOTE
     installed size is 50.1Mb
     sub-directories of 1Mb or more:
     libs 45.6Mb
     test_data 2.0Mb
     vignette_data 1.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [130s/159s]
    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) (2021-07-23 r80656)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Fedora 32 (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
    
     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
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.2.0 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.0 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.2.0
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-11 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.2.0 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Warning: namespace 'GLMMadaptive' is not available and has been replaced
     by .GlobalEnv when processing object 'fit'
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S....1.S
     trickier examples: SS.SSSS
     bootMer:
     bootMer: SS
     control: SS
     disp: ...
     downstream:
     emmeans: .............
     effects: ..
     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:
     basic methods: ...........................S.S....................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S........S.
     offset:
     offsets: SSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSSS..S...S..
     reml:
     REML: ......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .....S
     start: ..
     utils: .............
     varstruc:
     variance structures: ........SSS
     weight:
     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:57:3) - Reason: On CRAN
    
     3. Variance structures (test-basics.R:66:3) - Reason: On CRAN
    
     4. Multiple RE, reordering (test-basics.R:96:6) - Reason: On CRAN
    
     5. close to lme4 results (test-basics.R:131:5) - Reason: On CRAN
    
     6. basic zero inflation (test-basics.R:184:8) - Reason: On CRAN
    
     7. alternative binomial model specifications (test-basics.R:202:5) - Reason: On CRAN
    
     8. NA handling (test-basics.R:223:5) - Reason: On CRAN
    
     9. quine NB fit (test-basics.R:241:5) - Reason: On CRAN
    
     10. contrasts arg (test-basics.R:252:5) - Reason: On CRAN
    
     11. zero disp setting (test-basics.R:263:5) - Reason: On CRAN
    
     12. Bernoulli responses (test-bootMer.R:11:3) - Reason: On CRAN
    
     13. binomial responses (test-bootMer.R:21:5) - 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. beta (test-families.R:88:3) - Reason: On CRAN
    
     17. nbinom (test-families.R:110:5) - Reason: On CRAN
    
     18. dbetabinom (test-families.R:165:5) - Reason: On CRAN
    
     19. truncated (test-families.R:238:5) - Reason: On CRAN
    
     20. truncated_genpois (test-families.R:315:3) - Reason: On CRAN
    
     21. truncated_compois (test-families.R:332:5) - Reason: On CRAN
    
     22. compois (test-families.R:343:5) - Reason: On CRAN
    
     23. genpois (test-families.R:354:5) - Reason: On CRAN
    
     24. tweedie (test-families.R:363:5) - Reason: On CRAN
    
     25. anova ML/REML checks (test-methods.R:114:5) - Reason: On CRAN
    
     26. terms back-compatibility (test-methods.R:157:5) - Reason: skip until TMB fits are back-compatible
    
     27. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
    
     28. trunc nbinom sim 2 (test-methods.R:524:1) - Reason: empty test
    
     29. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
    
     30. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
    
     32. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
    
     34. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
    
     35. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
    
     36. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
    
     37. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
    
     38. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
    
     39. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
    
     40. two-column response (test-predict.R:64:5) - Reason: On CRAN
    
     41. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
    
     42. scale (test-predict.R:186:5) - Reason: On CRAN
    
     43. scale_RE (test-predict.R:208:5) - Reason: On CRAN
    
     44. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
    
     45. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
    
     46. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
    
     47. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
    
     48. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
    
     49. back-compatibility (test-sparseX.R:20:5) - Reason: skip until TMB fits are back-compatible
    
     50. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
    
     51. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
    
     52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
    
     53. zi (test-zi.R:12:3) - Reason: On CRAN
    
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 2.131994e-08
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [140s/192s]
    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) (2021-07-19 r80640)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Fedora 32 (Workstation Edition)
    
     Matrix products: default
     BLAS: /data/gannet/ripley/R/R-devel/lib/libRblas.so
     LAPACK: /data/gannet/ripley/R/R-devel/lib/libRlapack.so
    
     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
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.2.0 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.0 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.2.0
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-11 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.2.0 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S....1.S
     trickier examples: SS.SSSS
     bootMer:
     bootMer: SS
     control: SS
     disp: ...
     downstream:
     emmeans: .............
     effects: ..
     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:
     basic methods: ...........................S.S....................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S........S.
     offset:
     offsets: SSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSSS..S...S..
     reml:
     REML: ......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .....S
     start: ..
     utils: .............
     varstruc:
     variance structures: ........SSS
     weight:
     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:57:3) - Reason: On CRAN
    
     3. Variance structures (test-basics.R:66:3) - Reason: On CRAN
    
     4. Multiple RE, reordering (test-basics.R:96:6) - Reason: On CRAN
    
     5. close to lme4 results (test-basics.R:131:5) - Reason: On CRAN
    
     6. basic zero inflation (test-basics.R:184:8) - Reason: On CRAN
    
     7. alternative binomial model specifications (test-basics.R:202:5) - Reason: On CRAN
    
     8. NA handling (test-basics.R:223:5) - Reason: On CRAN
    
     9. quine NB fit (test-basics.R:241:5) - Reason: On CRAN
    
     10. contrasts arg (test-basics.R:252:5) - Reason: On CRAN
    
     11. zero disp setting (test-basics.R:263:5) - Reason: On CRAN
    
     12. Bernoulli responses (test-bootMer.R:11:3) - Reason: On CRAN
    
     13. binomial responses (test-bootMer.R:21:5) - 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. beta (test-families.R:88:3) - Reason: On CRAN
    
     17. nbinom (test-families.R:110:5) - Reason: On CRAN
    
     18. dbetabinom (test-families.R:165:5) - Reason: On CRAN
    
     19. truncated (test-families.R:238:5) - Reason: On CRAN
    
     20. truncated_genpois (test-families.R:315:3) - Reason: On CRAN
    
     21. truncated_compois (test-families.R:332:5) - Reason: On CRAN
    
     22. compois (test-families.R:343:5) - Reason: On CRAN
    
     23. genpois (test-families.R:354:5) - Reason: On CRAN
    
     24. tweedie (test-families.R:363:5) - Reason: On CRAN
    
     25. anova ML/REML checks (test-methods.R:114:5) - Reason: On CRAN
    
     26. terms back-compatibility (test-methods.R:157:5) - Reason: skip until TMB fits are back-compatible
    
     27. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
    
     28. trunc nbinom sim 2 (test-methods.R:524:1) - Reason: empty test
    
     29. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
    
     30. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
    
     32. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
    
     34. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
    
     35. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
    
     36. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
    
     37. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
    
     38. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
    
     39. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
    
     40. two-column response (test-predict.R:64:5) - Reason: On CRAN
    
     41. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
    
     42. scale (test-predict.R:186:5) - Reason: On CRAN
    
     43. scale_RE (test-predict.R:208:5) - Reason: On CRAN
    
     44. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
    
     45. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
    
     46. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
    
     47. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
    
     48. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
    
     49. back-compatibility (test-sparseX.R:20:5) - Reason: skip until TMB fits are back-compatible
    
     50. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
    
     51. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
    
     52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
    
     53. zi (test-zi.R:12:3) - Reason: On CRAN
    
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 2.131994e-08
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.2
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 18.2Mb
     sub-directories of 1Mb or more:
     libs 13.7Mb
     test_data 2.0Mb
     vignette_data 1.1Mb
Flavors: r-devel-windows-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [113s/123s]
    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 4.1.0 Patched (2021-07-20 r80649)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Debian GNU/Linux 11 (bullseye)
    
     Matrix products: default
     BLAS: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib/libRblas.so
     LAPACK: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib/libRlapack.so
    
     locale:
     [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
     [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
     [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
     [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
     [9] LC_ADDRESS=C LC_TELEPHONE=C
     [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.1.0 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.0 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.1.0
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-11 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.1.0 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Warning: namespace 'GLMMadaptive' is not available and has been replaced
     by .GlobalEnv when processing object 'fit'
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S....1.S
     trickier examples: SS.SSSS
     bootMer:
     bootMer: SS
     control: SS
     disp: ...
     downstream:
     emmeans: .............
     effects: ..
     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:
     basic methods: ...........................S.S....................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S........S.
     offset:
     offsets: SSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSSS..S...S..
     reml:
     REML: ......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .....S
     start: ..
     utils: .............
     varstruc:
     variance structures: ........SSS
     weight:
     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:57:3) - Reason: On CRAN
    
     3. Variance structures (test-basics.R:66:3) - Reason: On CRAN
    
     4. Multiple RE, reordering (test-basics.R:96:6) - Reason: On CRAN
    
     5. close to lme4 results (test-basics.R:131:5) - Reason: On CRAN
    
     6. basic zero inflation (test-basics.R:184:8) - Reason: On CRAN
    
     7. alternative binomial model specifications (test-basics.R:202:5) - Reason: On CRAN
    
     8. NA handling (test-basics.R:223:5) - Reason: On CRAN
    
     9. quine NB fit (test-basics.R:241:5) - Reason: On CRAN
    
     10. contrasts arg (test-basics.R:252:5) - Reason: On CRAN
    
     11. zero disp setting (test-basics.R:263:5) - Reason: On CRAN
    
     12. Bernoulli responses (test-bootMer.R:11:3) - Reason: On CRAN
    
     13. binomial responses (test-bootMer.R:21:5) - 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. beta (test-families.R:88:3) - Reason: On CRAN
    
     17. nbinom (test-families.R:110:5) - Reason: On CRAN
    
     18. dbetabinom (test-families.R:165:5) - Reason: On CRAN
    
     19. truncated (test-families.R:238:5) - Reason: On CRAN
    
     20. truncated_genpois (test-families.R:315:3) - Reason: On CRAN
    
     21. truncated_compois (test-families.R:332:5) - Reason: On CRAN
    
     22. compois (test-families.R:343:5) - Reason: On CRAN
    
     23. genpois (test-families.R:354:5) - Reason: On CRAN
    
     24. tweedie (test-families.R:363:5) - Reason: On CRAN
    
     25. anova ML/REML checks (test-methods.R:114:5) - Reason: On CRAN
    
     26. terms back-compatibility (test-methods.R:157:5) - Reason: skip until TMB fits are back-compatible
    
     27. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
    
     28. trunc nbinom sim 2 (test-methods.R:524:1) - Reason: empty test
    
     29. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
    
     30. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
    
     32. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
    
     34. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
    
     35. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
    
     36. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
    
     37. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
    
     38. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
    
     39. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
    
     40. two-column response (test-predict.R:64:5) - Reason: On CRAN
    
     41. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
    
     42. scale (test-predict.R:186:5) - Reason: On CRAN
    
     43. scale_RE (test-predict.R:208:5) - Reason: On CRAN
    
     44. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
    
     45. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
    
     46. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
    
     47. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
    
     48. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
    
     49. back-compatibility (test-sparseX.R:20:5) - Reason: skip until TMB fits are back-compatible
    
     50. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
    
     51. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
    
     52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
    
     53. zi (test-zi.R:12:3) - Reason: On CRAN
    
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 2.131994e-08
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.1.2
Check: examples
Result: ERROR
    Running examples in ‘glmmTMB-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: VarCorr.glmmTMB
    > ### Title: Extract variance and correlation components
    > ### Aliases: VarCorr.glmmTMB VarCorr
    > ### Keywords: internal
    >
    > ### ** Examples
    >
    > ## Comparing variance-covariance matrix with manual computation
    > data("sleepstudy",package="lme4")
    > fm4 <- glmmTMB(Reaction ~ Days + (Days|Subject), sleepstudy)
    
     *** caught segfault ***
    address 4, cause 'memory not mapped'
    
     *** caught segfault ***
    address dc8e8034, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
    An irrecoverable exception occurred. R is aborting now ...
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [15s/45s]
    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 4.1.0 Patched (2021-07-16 r80640)
     Platform: i386-pc-solaris2.10 (32-bit)
     Running under: Solaris 10
    
     Matrix products: default
     BLAS: /home/ripley/R/cc/lib/libRblas.so
     LAPACK: /home/ripley/R/cc/lib/libRlapack.so
    
     locale:
     [1] /en_GB.UTF-8/C/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.1.0 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.0 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.1.0
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-11 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.1.0 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Warning: namespace 'GLMMadaptive' is not available and has been replaced
     by .GlobalEnv when processing object 'fit'
     Anova: ..
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     *** caught segfault ***
     address 29cecf48, cause 'memory not mapped'
    
     Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (1 | Subject), disp = ~I(Days > 5), sleepstudy, REML = FALSE)
     9: eval(code, test_env)
     10: eval(code, test_env)
     11: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     12: doTryCatch(return(expr), name, parentenv, handler)
     13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     15: doTryCatch(return(expr), name, parentenv, handler)
     16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     17: tryCatchList(expr, classes, parentenv, handlers)
     18: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     19: test_code(NULL, exprs, env)
     20: source_file(path, child_env(env), wrap = wrap)
     21: FUN(X[[i]], ...)
     22: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     23: force(code)
     24: doWithOneRestart(return(expr), restart)
     25: withOneRestart(expr, restarts[[1L]])
     26: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     27: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     28: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     29: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     30: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     31: test_check(pkg, reporter = "summary")
     An irrecoverable exception occurred. R is aborting now ...
    
     Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (1 | Subject), disp = ~I(Days > 5), sleepstudy, REML = FALSE)
     9: eval(code, test_env)
     10: eval(code, test_env)
     11: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     12: doTryCatch(return(expr), name, parentenv, handler)
     13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     15: doTryCatch(return(expr), name, parentenv, handler)
     16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     17: tryCatchList(expr, classes, parentenv, handlers)
     18: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     19: test_code(NULL, exprs, env)
     20: source_file(path, child_env(env), wrap = wrap)
     21: FUN(X[[i]], ...)
     22: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     23: force(code)
     24: doWithOneRestart(return(expr), restart)
     25: withOneRestart(expr, restarts[[1L]])
     26: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     27: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     28: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     29: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     30: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     31: test_check(pkg, reporter = "summary")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘covstruct.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘covstruct.rmd’
    
    --- re-building ‘mcmc.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘mcmc.rmd’
    
    Segmentation Fault - core dumped
    --- re-building ‘miscEx.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address c09534b8, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(y ~ x, family = beta_family(), data = dd)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
    18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: knit(input, text = text, envir = envir, quiet = quiet)
    27: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    28: vweave(...)
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    34: tools:::.buildOneVignette("miscEx.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "miscEx", "UTF-8", "/tmp/RtmpoWayWo/working_dir/RtmpZjaqbR/file560a24ba6eea.rds")
    An irrecoverable exception occurred. R is aborting now ...
    
     *** caught segfault ***
    address 1b0, cause 'memory not mapped'
    --- re-building ‘parallel.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘parallel.Rmd’
    
    Segmentation Fault - core dumped
    --- re-building ‘sim.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address 3c, cause 'memory not mapped'
    
    Traceback:
     1: sparseHessianFun(env, skipFixedEffects = skipFixedEffects)
     2: he(par)
     3: newton(par = c(b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0), fn = function (par.random, order = 0, ...) { par[random] <- par.random par[-random] <- par.fixed res <- f(par, order = order, ...) switch(order + 1, res, res[random], res[random, random])}, gr = function (x) f0(x, order = 1), he = function (par.random) { par[random] <- par.random par[-random] <- par.fixed spHess(par, random = TRUE)}, env = <environment>, maxit = 1000, trace = FALSE)
     4: do.call("newton", c(list(par = eval(random.start), fn = f0, gr = function(x) f0(x, order = 1), he = H0, env = env), inner.control))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
     9: try(do.call("newton", c(list(par = eval(random.start), fn = f0, gr = function(x) f0(x, order = 1), he = H0, env = env), inner.control)), silent = silent)
    10: ff(x, order = 0)
    11: doTryCatch(return(expr), name, parentenv, handler)
    12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    13: tryCatchList(expr, classes, parentenv, handlers)
    14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
    15: try({ if (MCcontrol$doMC) { ff(x, order = 0) MC(last.par, n = MCcontrol$n, seed = MCcontrol$seed, order = 0) } else ff(x, order = 0)}, silent = silent)
    16: obj$fn(obj$par)
    17: fitTMB(TMBStruc)
    18: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), family = nbinom1, ziformula = ~1, data = Owls)
    19: eval(expr, envir, enclos)
    20: eval(expr, envir, enclos)
    21: withVisible(eval(expr, envir, enclos))
    22: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    23: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    24: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    25: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    26: evaluate::evaluate(...)
    27: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
    28: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    29: eng_r(options)
    30: block_exec(params)
    31: call_block(x)
    32: process_group.block(group)
    33: process_group(group)
    34: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    35: process_file(text, output)
    36: knit(input, text = text, envir = envir, quiet = quiet)
    37: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    38: vweave(...)
    39: engine$weave(file, quiet = quiet, encoding = enc)
    40: doTryCatch(return(expr), name, parentenv, handler)
    41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    42: tryCatchList(expr, classes, parentenv, handlers)
    43: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    44: tools:::.buildOneVignette("sim.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "sim", "UTF-8", "/tmp/RtmpoWayWo/working_dir/RtmpZjaqbR/file560a4dda274b.rds")
    An irrecoverable exception occurred. R is aborting now ...
    Segmentation Fault - core dumped
    --- re-building ‘troubleshooting.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(formula = taeCPUE ~ Avg.Relief + (1 | site.name/reef.name), data = dd, family = nbinom1, ziformula = ~0, dispformula = ~1, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
     9: eval(call, parent.frame())
    10: eval(call, parent.frame())
    11: update.default(mod2, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
    12: update(mod2, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
    13: eval(expr, envir, enclos)
    14: eval(expr, envir, enclos)
    15: withVisible(eval(expr, envir, enclos))
    16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    20: evaluate::evaluate(...)
    21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
    22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    23: eng_r(options)
    24: block_exec(params)
    25: call_block(x)
    26: process_group.block(group)
    27: process_group(group)
    28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    29: process_file(text, output)
    30: knit(input, text = text, envir = envir, quiet = quiet)
    31: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    32: vweave(...)
    33: engine$weave(file, quiet = quiet, encoding = enc)
    34: doTryCatch(return(expr), name, parentenv, handler)
    35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    36: tryCatchList(expr, classes, parentenv, handlers)
    37: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    38: tools:::.buildOneVignette("troubleshooting.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "troubleshooting", "UTF-8", "/tmp/RtmpoWayWo/working_dir/RtmpZjaqbR/file560a305d7623.rds")
    An irrecoverable exception occurred. R is aborting now ...
    --- re-building ‘glmmTMB.Rnw’ using knitr
    Loading required package: stats4
    --- finished re-building ‘glmmTMB.Rnw’
    
    Segmentation Fault - core dumped
    --- re-building ‘model_evaluation.Rnw’ using knitr
    Loading required package: carData
    lattice theme set by effectsTheme()
    See ?effectsTheme for details.
    Loading required package: mvtnorm
    Loading required package: survival
    Loading required package: TH.data
    Loading required package: MASS
    
    Attaching package: 'TH.data'
    
    The following object is masked from 'package:MASS':
    
     geyser
    
    This is DHARMa 0.4.3. For overview type '?DHARMa'. For recent changes, type news(package = 'DHARMa') Note: Syntax of plotResiduals has changed in 0.3.0, see ?plotResiduals for details
    Loading required package: ggplot2
    Version: 1.37.5
    Date: 2020-06-17
    Author: Philip Leifeld (University of Essex)
    
    Consider submitting praise using the praise or praise_interactive functions.
    Please cite the JSS article in your publications -- see citation("texreg").
    
     *** caught segfault ***
    address bb9ca804, cause 'memory not mapped'
    
     *** caught segfault ***
    address 4, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), contrasts = list(FoodTreatment = "contr.sum", SexParent = "contr.sum"), family = nbinom1, zi = ~1, data = Owls)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
    18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    27: engine$weave(file, quiet = quiet, encoding = enc)
    28: doTryCatch(return(expr), name, parentenv, handler)
    29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    30: tryCatchList(expr, classes, parentenv, handlers)
    31: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    32: tools:::.buildOneVignette("model_evaluation.Rnw", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "model_evaluation", "UTF-8", "/tmp/RtmpoWayWo/working_dir/RtmpZjaqbR/file560a1f92e45.rds")
    An irrecoverable exception occurred. R is aborting now ...
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), contrasts = list(FoodTreatment = "contr.sum", SexParent = "contr.sum"), family = nbinom1, zi = ~1, data = Owls)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
    18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    27: engine$weave(file, quiet = quiet, encoding = enc)
    28: doTryCatch(return(expr), name, parentenv, handler)
    29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    30: tryCatchList(expr, classes, parentenv, handlers)
    31: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    32: tools:::.buildOneVignette("model_evaluation.Rnw", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "model_evaluation", "UTF-8", "/tmp/RtmpoWayWo/working_dir/RtmpZjaqbR/file560a1f92e45.rds")
    An irrecoverable exception occurred. R is aborting now ...
    SUMMARY: processing the following files failed:
     ‘miscEx.rmd’ ‘sim.rmd’ ‘troubleshooting.rmd’ ‘model_evaluation.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [108s/120s]
    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 4.1.0 (2021-05-18)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Debian GNU/Linux 11 (bullseye)
    
     Matrix products: default
     BLAS: /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libRblas.so
     LAPACK: /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libRlapack.so
    
     locale:
     [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
     [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
     [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
     [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
     [9] LC_ADDRESS=C LC_TELEPHONE=C
     [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.1.0 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.0 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.1.0
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-11 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.1.0 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Warning: namespace 'GLMMadaptive' is not available and has been replaced
     by .GlobalEnv when processing object 'fit'
     Anova: ..............
     VarCorr: .............
     altopt:
     alternative optimizers: S
     basics: .............SS.....S....1.S
     trickier examples: SS.SSSS
     bootMer:
     bootMer: SS
     control: SS
     disp: ...
     downstream:
     emmeans: .............
     effects: ..
     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:
     basic methods: ...........................S.S....................................
     simulate consistency with glm/lm: ...
     Ranef etc.: .......S........S.
     offset:
     offsets: SSSSSSSS
     predict: .....SSS
     Predict two-column response case: SS.................S..SSSS..S...S..
     reml:
     REML: ......
     rr: .........
     saveload:
     Saving and loading glmmTMB objects: .
     sparseX:
     sparse X models: .....S
     start: ..
     utils: .............
     varstruc:
     variance structures: ........SSS
     weight:
     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:57:3) - Reason: On CRAN
    
     3. Variance structures (test-basics.R:66:3) - Reason: On CRAN
    
     4. Multiple RE, reordering (test-basics.R:96:6) - Reason: On CRAN
    
     5. close to lme4 results (test-basics.R:131:5) - Reason: On CRAN
    
     6. basic zero inflation (test-basics.R:184:8) - Reason: On CRAN
    
     7. alternative binomial model specifications (test-basics.R:202:5) - Reason: On CRAN
    
     8. NA handling (test-basics.R:223:5) - Reason: On CRAN
    
     9. quine NB fit (test-basics.R:241:5) - Reason: On CRAN
    
     10. contrasts arg (test-basics.R:252:5) - Reason: On CRAN
    
     11. zero disp setting (test-basics.R:263:5) - Reason: On CRAN
    
     12. Bernoulli responses (test-bootMer.R:11:3) - Reason: On CRAN
    
     13. binomial responses (test-bootMer.R:21:5) - 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. beta (test-families.R:88:3) - Reason: On CRAN
    
     17. nbinom (test-families.R:110:5) - Reason: On CRAN
    
     18. dbetabinom (test-families.R:165:5) - Reason: On CRAN
    
     19. truncated (test-families.R:238:5) - Reason: On CRAN
    
     20. truncated_genpois (test-families.R:315:3) - Reason: On CRAN
    
     21. truncated_compois (test-families.R:332:5) - Reason: On CRAN
    
     22. compois (test-families.R:343:5) - Reason: On CRAN
    
     23. genpois (test-families.R:354:5) - Reason: On CRAN
    
     24. tweedie (test-families.R:363:5) - Reason: On CRAN
    
     25. anova ML/REML checks (test-methods.R:114:5) - Reason: On CRAN
    
     26. terms back-compatibility (test-methods.R:157:5) - Reason: skip until TMB fits are back-compatible
    
     27. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
    
     28. trunc nbinom sim 2 (test-methods.R:524:1) - Reason: empty test
    
     29. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
    
     30. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
    
     31. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
    
     32. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
    
     33. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
    
     34. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
    
     35. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
    
     36. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
    
     37. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
    
     38. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
    
     39. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
    
     40. two-column response (test-predict.R:64:5) - Reason: On CRAN
    
     41. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
    
     42. scale (test-predict.R:186:5) - Reason: On CRAN
    
     43. scale_RE (test-predict.R:208:5) - Reason: On CRAN
    
     44. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
    
     45. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
    
     46. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
    
     47. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
    
     48. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
    
     49. back-compatibility (test-sparseX.R:20:5) - Reason: skip until TMB fits are back-compatible
    
     50. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
    
     51. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
    
     52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
    
     53. zi (test-zi.R:12:3) - Reason: On CRAN
    
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 2.131994e-08
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64

Version: 1.1.1
Check: installed package size
Result: NOTE
     installed size is 73.2Mb
     sub-directories of 1Mb or more:
     doc 1.1Mb
     libs 69.9Mb
     vignette_data 1.1Mb
Flavor: r-release-macos-arm64

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [51s/52s]
    Running the tests in ‘tests/AAAtest-all.R’ failed.
    Last 13 lines of output:
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 1.492101e-08
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     In addition: Warning message:
     In checkMatrixPackageVersion() : Package version inconsistency detected.
     TMB was built with Matrix version 1.3.3
     Current Matrix version is 1.3.4
     Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
     Execution halted
Flavor: r-release-macos-x86_64

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [51s/51s]
    Running the tests in ‘tests/AAAtest-all.R’ failed.
    Last 13 lines of output:
     54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
     `gm1` not equal to matchForm(gm1, gm1u).
     Component "sdr": Component "gradient.fixed": Mean relative difference: 1.492101e-08
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     In addition: Warning message:
     In checkMatrixPackageVersion() : Package version inconsistency detected.
     TMB was built with Matrix version 1.3.2
     Current Matrix version is 1.3.4
     Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
     Execution halted
Flavor: r-oldrel-macos-x86_64