Last updated on 2021-07-26 02:48:51 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 | 160.70 | 236.01 | 396.71 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.2 | 624.66 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.2 | 648.30 | 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 | 1.1.2 | ERROR | ||||
| r-release-macos-x86_64 | 1.1.2 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 1.1.2 | 287.00 | 389.00 | 676.00 | NOTE | --no-vignettes |
| 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 |
ATLAS gcc11 M1mac MKL noLD OpenBLAS
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-arm64, 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’ [137s/160s]
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) (2021-07-24 r80661)
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-release-windows-ix86+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: 1.1.2
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [44s/53s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Last 13 lines of output:
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: 2.287797e-08
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-release-macos-arm64
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$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mcmc.rmd’
--- re-building ‘miscEx.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘miscEx.rmd’
--- re-building ‘parallel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘parallel.Rmd’
--- re-building ‘sim.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 47-49 (sim.rmd)
Error: processing vignette 'sim.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sim.rmd’
--- 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.
--- finished re-building ‘troubleshooting.rmd’
--- re-building ‘glmmTMB.Rnw’ using knitr
Loading required package: stats4
--- finished re-building ‘glmmTMB.Rnw’
--- 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 0.4.1. 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").
Attaching package: 'huxtable'
The following objects are masked from 'package:xtable':
align, align<-, caption, caption<-, label, label<-, sanitize
The following object is masked from 'package:ggplot2':
theme_grey
--- finished re-building ‘model_evaluation.Rnw’
SUMMARY: processing the following file failed:
‘sim.rmd’
Error: Vignette re-building failed.
Execution halted
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