Last updated on 2023-03-27 03:53:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.6 | 260.58 | 318.98 | 579.56 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.6 | 224.42 | 246.06 | 470.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.6 | 776.96 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.6 | 796.08 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.6 | 264.00 | 343.00 | 607.00 | NOTE | --no-vignettes |
| r-patched-linux-x86_64 | 1.1.6 | 229.45 | 315.55 | 545.00 | ERROR | |
| r-release-linux-x86_64 | 1.1.6 | 205.76 | 301.78 | 507.54 | OK | |
| r-release-macos-arm64 | 1.1.6 | 153.00 | NOTE | |||
| r-release-macos-x86_64 | 1.1.6 | 242.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.6 | 242.00 | 192.00 | 434.00 | NOTE | --no-vignettes |
| r-oldrel-macos-arm64 | 1.1.6 | 190.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.1.6 | 256.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 1.1.6 | 568.00 | 472.00 | 1040.00 | NOTE | --no-vignettes |
Version: 1.1.6
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [74s/114s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Complete output:
> if (require("testthat")) {
+ pkg <- "glmmTMB"
+ require(pkg, character.only=TRUE)
+ print(sessionInfo())
+ test_check(pkg, reporter="summary")
+ print(warnings()) # TODO? catch most of these by expect_warning(..)
+ } else {
+ warnings("Package 'testthat' not available, cannot run unit tests for package",
+ sQuote(pkg))
+ }
Loading required package: testthat
Loading required package: glmmTMB
R Under development (unstable) (2023-03-24 r84048)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Vienna
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmmTMB_1.1.6 testthat_3.1.7
loaded via a namespace (and not attached):
[1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
[4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
[7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2
[10] lme4_1.1-32 brio_1.1.3 grid_4.4.0
[13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
[16] compiler_4.4.0 multcomp_1.4-23 codetools_0.2-19
[19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
[22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
[25] R6_2.5.1 splines_4.4.0 magrittr_2.0.3
[28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
Anova: ..............
VarCorr: .............
altopt:
alternative optimizers: S
basics: .............SS.....S12..3.S
trickier examples: SS.SSSS......
bootMer:
bootMer: SS
checkRank: ..................................W......W..
control: SS
diagnose: .S
disp: ...
downstream: S..
edgecases:
test edge cases: .
env:
basic examples: ...
families:
alternative binomial specifications: ..........
non-integer count warnings: .......
fitting exotic families: SSSSS
trunc compois: S
compois: S
genpois: S
tweedie: S.
link function info available: ............
link info added to family: ......
formulas:
formula parsing: ................
mapopt:
methods: ............................S....................................................
simulate consistency with glm/lm: ...
Ranef etc.: .......S.............
misc: .
offset: SSSSSSSSS
predict: .....SSS
Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
reml:
REML: .......
rr: .........
saveload:
Saving and loading glmmTMB objects: .
sparseX:
sparse X models: .......
start: ..
utils: ..............
varstruc:
variance structures: ........SSS.
weight: .........
zi:
ZI models: SS
══ Skipped ═════════════════════════════════════════════════════════════════════
1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:274:5') - Reason: On CRAN
12. Bernoulli responses ('test-bootMer.R:12:3') - Reason: On CRAN
13. binomial responses ('test-bootMer.R:22:5') - Reason: On CRAN
14. profile method ('test-control.R:16:3') - Reason: On CRAN
15. parallel regions ('test-control.R:50:3') - Reason: On CRAN
16. diagnose works with Tweedie fits ('test-diagnose.R:16:5') - Reason: On CRAN
17. emmeans ('test-downstream.R:8:5') - Reason: On CRAN
18. beta ('test-families.R:90:3') - Reason: On CRAN
19. nbinom ('test-families.R:112:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
21. truncated ('test-families.R:240:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
24. compois ('test-families.R:345:5') - Reason: On CRAN
25. genpois ('test-families.R:356:5') - Reason: On CRAN
26. tweedie ('test-families.R:365:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
43. scale ('test-predict.R:183:5') - Reason: On CRAN
44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
54. zi ('test-zi.R:12:3') - Reason: On CRAN
55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Warnings ════════════════════════════════════════════════════════════════════
1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
`gm0` not equal to `res_chr`.
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
`gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
`gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.6
Check: installed package size
Result: NOTE
installed size is 11.4Mb
sub-directories of 1Mb or more:
doc 1.3Mb
libs 6.2Mb
test_data 2.2Mb
vignette_data 1.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.1.6
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [110s/270s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Complete output:
> if (require("testthat")) {
+ pkg <- "glmmTMB"
+ require(pkg, character.only=TRUE)
+ print(sessionInfo())
+ test_check(pkg, reporter="summary")
+ print(warnings()) # TODO? catch most of these by expect_warning(..)
+ } else {
+ warnings("Package 'testthat' not available, cannot run unit tests for package",
+ sQuote(pkg))
+ }
Loading required package: testthat
Loading required package: glmmTMB
R Under development (unstable) (2023-03-25 r84059)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora Linux 36 (Workstation Edition)
Matrix products: default
BLAS: /data/gannet/ripley/R/R-devel/lib/libRblas.so
LAPACK: /usr/lib64/liblapack.so.3.10.1
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmmTMB_1.1.6 testthat_3.1.7
loaded via a namespace (and not attached):
[1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
[4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
[7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2
[10] lme4_1.1-32 brio_1.1.3 grid_4.4.0
[13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
[16] compiler_4.4.0 multcomp_1.4-23 codetools_0.2-19
[19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
[22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
[25] R6_2.5.1 splines_4.4.0 magrittr_2.0.3
[28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
Anova: ..............
VarCorr: .............
altopt:
alternative optimizers: S
basics: .............SS.....S12..3.S
trickier examples: SS.SSSS......
bootMer:
bootMer: SS
checkRank: ..................................W......W..
control: SS
diagnose: .S
disp: ...
downstream: S..
edgecases:
test edge cases: .
env:
basic examples: ...
families:
alternative binomial specifications: ..........
non-integer count warnings: .......
fitting exotic families: SSSSS
trunc compois: S
compois: S
genpois: S
tweedie: S.
link function info available: ............
link info added to family: ......
formulas:
formula parsing: ................
mapopt:
methods: ............................S....................................................
simulate consistency with glm/lm: ...
Ranef etc.: .......S.............
misc: .
offset: SSSSSSSSS
predict: .....SSS
Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
reml:
REML: .......
rr: .........
saveload:
Saving and loading glmmTMB objects: .
sparseX:
sparse X models: .......
start: ..
utils: ..............
varstruc:
variance structures: ........SSS.
weight: .........
zi:
ZI models: SS
══ Skipped ═════════════════════════════════════════════════════════════════════
1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:274:5') - Reason: On CRAN
12. Bernoulli responses ('test-bootMer.R:12:3') - Reason: On CRAN
13. binomial responses ('test-bootMer.R:22:5') - Reason: On CRAN
14. profile method ('test-control.R:16:3') - Reason: On CRAN
15. parallel regions ('test-control.R:50:3') - Reason: On CRAN
16. diagnose works with Tweedie fits ('test-diagnose.R:16:5') - Reason: On CRAN
17. emmeans ('test-downstream.R:8:5') - Reason: On CRAN
18. beta ('test-families.R:90:3') - Reason: On CRAN
19. nbinom ('test-families.R:112:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
21. truncated ('test-families.R:240:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
24. compois ('test-families.R:345:5') - Reason: On CRAN
25. genpois ('test-families.R:356:5') - Reason: On CRAN
26. tweedie ('test-families.R:365:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
43. scale ('test-predict.R:183:5') - Reason: On CRAN
44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
54. zi ('test-zi.R:12:3') - Reason: On CRAN
55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Warnings ════════════════════════════════════════════════════════════════════
1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
`gm0` not equal to `res_chr`.
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
`gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
`gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.6
Flags: --no-vignettes
Check: installed package size
Result: NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
doc 1.3Mb
libs 4.3Mb
test_data 2.2Mb
vignette_data 1.1Mb
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.1.6
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [90s/103s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Complete output:
> if (require("testthat")) {
+ pkg <- "glmmTMB"
+ require(pkg, character.only=TRUE)
+ print(sessionInfo())
+ test_check(pkg, reporter="summary")
+ print(warnings()) # TODO? catch most of these by expect_warning(..)
+ } else {
+ warnings("Package 'testthat' not available, cannot run unit tests for package",
+ sQuote(pkg))
+ }
Loading required package: testthat
Loading required package: glmmTMB
R version 4.3.0 alpha (2023-03-24 r84048)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid
Matrix products: default
BLAS: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Vienna
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmmTMB_1.1.6 testthat_3.1.7
loaded via a namespace (and not attached):
[1] nlme_3.1-162 cli_3.6.1 rlang_1.1.0
[4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4
[7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2
[10] lme4_1.1-32 brio_1.1.3 grid_4.3.0
[13] MASS_7.3-58.3 mvtnorm_1.1-3 numDeriv_2016.8-1.1
[16] compiler_4.3.0 multcomp_1.4-23 codetools_0.2-19
[19] sandwich_3.0-2 emmeans_1.8.5 coda_0.19-4
[22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3
[25] R6_2.5.1 splines_4.3.0 magrittr_2.0.3
[28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-5
Anova: ..............
VarCorr: .............
altopt:
alternative optimizers: S
basics: .............SS.....S12..3.S
trickier examples: SS.SSSS......
bootMer:
bootMer: SS
checkRank: ..................................W......W..
control: SS
diagnose: .S
disp: ...
downstream: S..
edgecases:
test edge cases: .
env:
basic examples: ...
families:
alternative binomial specifications: ..........
non-integer count warnings: .......
fitting exotic families: SSSSS
trunc compois: S
compois: S
genpois: S
tweedie: S.
link function info available: ............
link info added to family: ......
formulas:
formula parsing: ................
mapopt:
methods: ............................S....................................................
simulate consistency with glm/lm: ...
Ranef etc.: .......S.............
misc: .
offset: SSSSSSSSS
predict: .....SSS
Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
reml:
REML: .......
rr: .........
saveload:
Saving and loading glmmTMB objects: .
sparseX:
sparse X models: .......
start: ..
utils: ..............
varstruc:
variance structures: ........SSS.
weight: .........
zi:
ZI models: SS
══ Skipped ═════════════════════════════════════════════════════════════════════
1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:274:5') - Reason: On CRAN
12. Bernoulli responses ('test-bootMer.R:12:3') - Reason: On CRAN
13. binomial responses ('test-bootMer.R:22:5') - Reason: On CRAN
14. profile method ('test-control.R:16:3') - Reason: On CRAN
15. parallel regions ('test-control.R:50:3') - Reason: On CRAN
16. diagnose works with Tweedie fits ('test-diagnose.R:16:5') - Reason: On CRAN
17. emmeans ('test-downstream.R:8:5') - Reason: On CRAN
18. beta ('test-families.R:90:3') - Reason: On CRAN
19. nbinom ('test-families.R:112:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
21. truncated ('test-families.R:240:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
24. compois ('test-families.R:345:5') - Reason: On CRAN
25. genpois ('test-families.R:356:5') - Reason: On CRAN
26. tweedie ('test-families.R:365:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
43. scale ('test-predict.R:183:5') - Reason: On CRAN
44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
54. zi ('test-zi.R:12:3') - Reason: On CRAN
55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Warnings ════════════════════════════════════════════════════════════════════
1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
`gm0` not equal to `res_chr`.
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
`gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
`gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64