Last updated on 2025-08-05 12:49:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.11 | 230.54 | 355.56 | 586.10 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.11 | 187.76 | 277.66 | 465.42 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.11 | 1136.36 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.11 | 1050.73 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.11 | 228.00 | 328.00 | 556.00 | OK | --no-vignettes |
| r-patched-linux-x86_64 | 1.1.11 | 263.66 | 344.68 | 608.34 | OK | |
| r-release-linux-x86_64 | 1.1.11 | 250.22 | 344.18 | 594.40 | OK | |
| r-release-macos-arm64 | 1.1.11 | 255.00 | OK | |||
| r-release-macos-x86_64 | 1.1.11 | 562.00 | OK | |||
| r-release-windows-x86_64 | 1.1.11 | 222.00 | 326.00 | 548.00 | OK | --no-vignettes |
| r-oldrel-macos-arm64 | 1.1.11 | 262.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.1.11 | 531.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.11 | 280.00 | 375.00 | 655.00 | NOTE | --no-vignettes |
Version: 1.1.11
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [118s/132s]
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) (2025-08-03 r88495)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 13 (trixie)
Matrix products: default
BLAS: /home/hornik/tmp/R.check/r-devel-clang/Work/build/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1; LAPACK version 3.12.0
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_1.1.11 testthat_3.2.3
loaded via a namespace (and not attached):
[1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-3
[4] rlang_1.1.6 estimability_1.5.1 reformulas_0.4.1
[7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-14
[10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5
[13] grid_4.6.0 MASS_7.3-65 mvtnorm_1.3-3
[16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.6.0
[19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.2
[22] coda_0.19-4.1 Rcpp_1.1.0 mgcv_1.9-3
[25] lattice_0.22-7 nloptr_2.2.1 R6_2.6.1
[28] Rdpack_2.6.4 splines_4.6.0 rbibutils_2.3
[31] magrittr_2.0.3 Matrix_1.7-3 tools_4.6.0
[34] boot_1.3-31 survival_3.8-3
Anova: ...............
VarCorr: ...............
altopt:
alternative optimizers: S
basics: .............SS.....S......S
trickier examples: SS.SSSS...........
bootMer:
bootMer: SS
checkRank: ................................................
control: SS.....
diagnose: .S..
disp: ...
downstream: S.....
edgecases:
test edge cases: .
env:
basic examples: ...
families: .....................SSSSSSSSS.......................................
formulas:
formula parsing: ................
mapequal: ........
mapopt:
methods: ...............................S..........................................S..............S..............................
misc: .
offset: SSSSSSSSS
predict: .....SSSSS.................S..SSS....S..S...S.............S........
priors: ...........SS
propto: ......
reml: ........
rr: ..........
saveload:
Saving and loading glmmTMB objects: .
simulate: .........
simulate_new: ....S.........
smooths: 1...
sparseX:
sparse X models: .......
start: ..
utils: .........................................................................................................
varstruc: .........SSS.S
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:85:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:94:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:124:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:164:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:217:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:236:5') - Reason: On CRAN
8. NA handling ('test-basics.R:257:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:275:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:286:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:297:5') - 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:22:5') - Reason: On CRAN
18. beta ('test-families.R:103:3') - Reason: On CRAN
19. nbinom ('test-families.R:125:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:186:5') - Reason: On CRAN
21. truncated ('test-families.R:259:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:336:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:352:5') - Reason: On CRAN
24. compois ('test-families.R:362:5') - Reason: On CRAN
25. genpois ('test-families.R:372:5') - Reason: On CRAN
26. tweedie ('test-families.R:380:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN
28. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test
29. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN
30. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
31. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
32. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
33. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
34. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
35. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
36. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
37. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
38. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
39. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
40. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
41. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
42. two-column response ('test-predict.R:59:5') - Reason: On CRAN
43. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN
44. scale ('test-predict.R:181:5') - Reason: On CRAN
45. scale_RE ('test-predict.R:203:5') - Reason: On CRAN
46. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN
47. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN
48. contrasts carried over ('test-predict.R:291:5') - Reason: On CRAN
49. offset-only model (GH #625) ('test-predict.R:330:5') - Reason: On CRAN
50. inverse-link prediction ('test-predict.R:349:3') - Reason: On CRAN
51. nzprob doesn't segfault ('test-predict.R:440:5') - Reason: On CRAN
52. prior specs ('test-priors.R:125:5') - Reason: On CRAN
53. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test
54. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test
55. ar1 requires factor time ('test-varstruc.R:66:3') - Reason: On CRAN
56. varcorr_print ('test-varstruc.R:86:5') - Reason: On CRAN
57. cov_struct_order ('test-varstruc.R:139:5') - Reason: On CRAN
58. het ar1 ('test-varstruc.R:156:5') - Reason: On CRAN
59. zi ('test-zi.R:12:3') - Reason: On CRAN
60. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Error ('test-smooths.R:13:5'): basic smooth ──────────────────────────────
Error in ``[<-.ts`(`*tmp*`, ri, value = structure(c(1871, 1872, 1873, 1874,
1875, 1876, 1877, 1878, 1879, 1880, 1881, 1882, 1883, 1884, 1885,
1886, 1887, 1888, 1889, 1890, 1891, 1892, 1893, 1894, 1895, 1896,
1897, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907,
1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918,
1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929,
1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940,
1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951,
1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962,
1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970), tsp = c(1871,
1970, 1), class = "ts"))`: only replacement of elements is allowed
Backtrace:
▆
1. ├─testthat::expect_equal(predict(sm1), predict(sm1, newdata = ndat)) at test-smooths.R:13:5
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::predict(sm1, newdata = ndat)
5. └─glmmTMB:::predict.glmmTMB(sm1, newdata = ndat)
6. └─base::rbind(object$frame, newFr)
7. └─base::rbind(deparse.level, ...)
8. ├─base::`[<-`(`*tmp*`, ri, value = `<ts>`)
9. └─stats:::`[<-.ts`(`*tmp*`, ri, value = `<ts>`)
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.11
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [103s/126s]
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) (2025-08-03 r88495)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 13 (trixie)
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.3.12.1; LAPACK version 3.12.0
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_1.1.11 testthat_3.2.3
loaded via a namespace (and not attached):
[1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-3
[4] rlang_1.1.6 estimability_1.5.1 reformulas_0.4.1
[7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-14
[10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5
[13] grid_4.6.0 MASS_7.3-65 mvtnorm_1.3-3
[16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.6.0
[19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.2
[22] coda_0.19-4.1 Rcpp_1.1.0 mgcv_1.9-3
[25] lattice_0.22-7 nloptr_2.2.1 R6_2.6.1
[28] Rdpack_2.6.4 splines_4.6.0 rbibutils_2.3
[31] magrittr_2.0.3 Matrix_1.7-3 tools_4.6.0
[34] boot_1.3-31 survival_3.8-3
Anova: ...............
VarCorr: ...............
altopt:
alternative optimizers: S
basics: .............SS.....S......S
trickier examples: SS.SSSS...........
bootMer:
bootMer: SS
checkRank: ................................................
control: SS.....
diagnose: .S..
disp: ...
downstream: S.....
edgecases:
test edge cases: .
env:
basic examples: ...
families: .....................SSSSSSSSS.......................................
formulas:
formula parsing: ................
mapequal: ........
mapopt:
methods: ...............................S..........................................S..............S..............................
misc: .
offset: SSSSSSSSS
predict: .....SSSSS.................S..SSS....S..S...S.............S........
priors: ...........SS
propto: ......
reml: ........
rr: ..........
saveload:
Saving and loading glmmTMB objects: .
simulate: .........
simulate_new: ....S.........
smooths: 1...
sparseX:
sparse X models: .......
start: ..
utils: .........................................................................................................
varstruc: .........SSS.S
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:85:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:94:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:124:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:164:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:217:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:236:5') - Reason: On CRAN
8. NA handling ('test-basics.R:257:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:275:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:286:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:297:5') - 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:22:5') - Reason: On CRAN
18. beta ('test-families.R:103:3') - Reason: On CRAN
19. nbinom ('test-families.R:125:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:186:5') - Reason: On CRAN
21. truncated ('test-families.R:259:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:336:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:352:5') - Reason: On CRAN
24. compois ('test-families.R:362:5') - Reason: On CRAN
25. genpois ('test-families.R:372:5') - Reason: On CRAN
26. tweedie ('test-families.R:380:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN
28. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test
29. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN
30. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
31. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
32. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
33. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
34. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
35. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
36. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
37. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
38. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
39. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
40. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
41. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
42. two-column response ('test-predict.R:59:5') - Reason: On CRAN
43. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN
44. scale ('test-predict.R:181:5') - Reason: On CRAN
45. scale_RE ('test-predict.R:203:5') - Reason: On CRAN
46. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN
47. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN
48. contrasts carried over ('test-predict.R:291:5') - Reason: On CRAN
49. offset-only model (GH #625) ('test-predict.R:330:5') - Reason: On CRAN
50. inverse-link prediction ('test-predict.R:349:3') - Reason: On CRAN
51. nzprob doesn't segfault ('test-predict.R:440:5') - Reason: On CRAN
52. prior specs ('test-priors.R:125:5') - Reason: On CRAN
53. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test
54. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test
55. ar1 requires factor time ('test-varstruc.R:66:3') - Reason: On CRAN
56. varcorr_print ('test-varstruc.R:86:5') - Reason: On CRAN
57. cov_struct_order ('test-varstruc.R:139:5') - Reason: On CRAN
58. het ar1 ('test-varstruc.R:156:5') - Reason: On CRAN
59. zi ('test-zi.R:12:3') - Reason: On CRAN
60. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Error ('test-smooths.R:13:5'): basic smooth ──────────────────────────────
Error in ``[<-.ts`(`*tmp*`, ri, value = structure(c(1871, 1872, 1873, 1874,
1875, 1876, 1877, 1878, 1879, 1880, 1881, 1882, 1883, 1884, 1885,
1886, 1887, 1888, 1889, 1890, 1891, 1892, 1893, 1894, 1895, 1896,
1897, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907,
1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918,
1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929,
1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940,
1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951,
1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962,
1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970), tsp = c(1871,
1970, 1), class = "ts"))`: only replacement of elements is allowed
Backtrace:
▆
1. ├─testthat::expect_equal(predict(sm1), predict(sm1, newdata = ndat)) at test-smooths.R:13:5
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::predict(sm1, newdata = ndat)
5. └─glmmTMB:::predict.glmmTMB(sm1, newdata = ndat)
6. └─base::rbind(object$frame, newFr)
7. └─base::rbind(deparse.level, ...)
8. ├─base::`[<-`(`*tmp*`, ri, value = `<ts>`)
9. └─stats:::`[<-.ts`(`*tmp*`, ri, value = `<ts>`)
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.11
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [171s/177s]
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) (2025-08-05 r88508)
Platform: x86_64-pc-linux-gnu
Running under: Fedora Linux 42 (Workstation Edition)
Matrix products: default
BLAS: /data/gannet/ripley/R/R-clang/lib/libRblas.so
LAPACK: /data/gannet/ripley/R/R-clang/lib/libRlapack.so; LAPACK version 3.12.1
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_1.1.11 testthat_3.2.3
loaded via a namespace (and not attached):
[1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-3
[4] rlang_1.1.6 estimability_1.5.1 reformulas_0.4.1
[7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-14
[10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5
[13] grid_4.6.0 MASS_7.3-65 mvtnorm_1.3-3
[16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.6.0
[19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.2
[22] coda_0.19-4.1 Rcpp_1.1.0 mgcv_1.9-3
[25] lattice_0.22-7 nloptr_2.2.1 R6_2.6.1
[28] Rdpack_2.6.4 splines_4.6.0 rbibutils_2.3
[31] magrittr_2.0.3 Matrix_1.7-3 tools_4.6.0
[34] boot_1.3-31 survival_3.8-3
Anova: ...............
VarCorr: ...............
altopt:
alternative optimizers: S
basics: .............SS.....S......S
trickier examples: SS.SSSS...........
bootMer:
bootMer: SS
checkRank: ................................................
control: SS.....
diagnose: .S..
disp: ...
downstream: S.....
edgecases:
test edge cases: .
env:
basic examples: ...
families: .....................SSSSSSSSS.......................................
formulas:
formula parsing: ................
mapequal: ........
mapopt:
methods: ...............................S..........................................S..............S..............................
misc: .
offset: SSSSSSSSS
predict: .....SSSSS.................S..SSS....S..S...S.............S........
priors: ...........SS
propto: ......
reml: ........
rr: ..........
saveload:
Saving and loading glmmTMB objects: .
simulate: .........
simulate_new: ....S.........
smooths: 1...
sparseX:
sparse X models: .......
start: ..
utils: .........................................................................................................
varstruc: .........SSS.S
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:85:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:94:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:124:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:164:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:217:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:236:5') - Reason: On CRAN
8. NA handling ('test-basics.R:257:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:275:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:286:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:297:5') - 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:22:5') - Reason: On CRAN
18. beta ('test-families.R:103:3') - Reason: On CRAN
19. nbinom ('test-families.R:125:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:186:5') - Reason: On CRAN
21. truncated ('test-families.R:259:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:336:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:352:5') - Reason: On CRAN
24. compois ('test-families.R:362:5') - Reason: On CRAN
25. genpois ('test-families.R:372:5') - Reason: On CRAN
26. tweedie ('test-families.R:380:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN
28. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test
29. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN
30. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
31. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
32. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
33. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
34. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
35. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
36. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
37. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
38. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
39. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
40. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
41. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
42. two-column response ('test-predict.R:59:5') - Reason: On CRAN
43. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN
44. scale ('test-predict.R:181:5') - Reason: On CRAN
45. scale_RE ('test-predict.R:203:5') - Reason: On CRAN
46. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN
47. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN
48. contrasts carried over ('test-predict.R:291:5') - Reason: On CRAN
49. offset-only model (GH #625) ('test-predict.R:330:5') - Reason: On CRAN
50. inverse-link prediction ('test-predict.R:349:3') - Reason: On CRAN
51. nzprob doesn't segfault ('test-predict.R:440:5') - Reason: On CRAN
52. prior specs ('test-priors.R:125:5') - Reason: On CRAN
53. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test
54. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test
55. ar1 requires factor time ('test-varstruc.R:66:3') - Reason: On CRAN
56. varcorr_print ('test-varstruc.R:86:5') - Reason: On CRAN
57. cov_struct_order ('test-varstruc.R:139:5') - Reason: On CRAN
58. het ar1 ('test-varstruc.R:156:5') - Reason: On CRAN
59. zi ('test-zi.R:12:3') - Reason: On CRAN
60. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Error ('test-smooths.R:13:5'): basic smooth ──────────────────────────────
Error in ``[<-.ts`(`*tmp*`, ri, value = structure(c(1871, 1872, 1873, 1874,
1875, 1876, 1877, 1878, 1879, 1880, 1881, 1882, 1883, 1884, 1885,
1886, 1887, 1888, 1889, 1890, 1891, 1892, 1893, 1894, 1895, 1896,
1897, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907,
1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918,
1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929,
1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940,
1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951,
1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962,
1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970), tsp = c(1871,
1970, 1), class = "ts"))`: only replacement of elements is allowed
Backtrace:
▆
1. ├─testthat::expect_equal(predict(sm1), predict(sm1, newdata = ndat)) at test-smooths.R:13:5
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::predict(sm1, newdata = ndat)
5. └─glmmTMB:::predict.glmmTMB(sm1, newdata = ndat)
6. └─base::rbind(object$frame, newFr)
7. └─base::rbind(deparse.level, ...)
8. ├─base::`[<-`(`*tmp*`, ri, value = `<ts>`)
9. └─stats:::`[<-.ts`(`*tmp*`, ri, value = `<ts>`)
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.11
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [172s/194s]
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) (2025-08-05 r88508)
Platform: x86_64-pc-linux-gnu
Running under: Fedora Linux 42 (Workstation Edition)
Matrix products: default
BLAS: /data/gannet/ripley/R/R-devel/lib/libRblas.so
LAPACK: /usr/lib64/liblapack.so.3.12.0 LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmmTMB_1.1.11 testthat_3.2.3
loaded via a namespace (and not attached):
[1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-3
[4] rlang_1.1.6 estimability_1.5.1 reformulas_0.4.1
[7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-14
[10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5
[13] grid_4.6.0 MASS_7.3-65 mvtnorm_1.3-3
[16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.6.0
[19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.2
[22] coda_0.19-4.1 Rcpp_1.1.0 mgcv_1.9-3
[25] lattice_0.22-7 nloptr_2.2.1 R6_2.6.1
[28] Rdpack_2.6.4 splines_4.6.0 rbibutils_2.3
[31] magrittr_2.0.3 Matrix_1.7-3 tools_4.6.0
[34] boot_1.3-31 survival_3.8-3
Anova: ...............
VarCorr: ...............
altopt:
alternative optimizers: S
basics: .............SS.....S......S
trickier examples: SS.SSSS...........
bootMer:
bootMer: SS
checkRank: ................................................
control: SS.....
diagnose: .S..
disp: ...
downstream: S.....
edgecases:
test edge cases: .
env:
basic examples: ...
families: .....................SSSSSSSSS.......................................
formulas:
formula parsing: ................
mapequal: ........
mapopt:
methods: ...............................S..........................................S..............S..............................
misc: .
offset: SSSSSSSSS
predict: .....SSSSS.................S..SSS....S..S...S.............S........
priors: ...........SS
propto: ......
reml: ........
rr: ..........
saveload:
Saving and loading glmmTMB objects: .
simulate: .........
simulate_new: ....S.........
smooths: 1...
sparseX:
sparse X models: .......
start: ..
utils: .........................................................................................................
varstruc: .........SSS.S
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:85:3') - Reason: On CRAN
3. Variance structures ('test-basics.R:94:3') - Reason: On CRAN
4. Multiple RE, reordering ('test-basics.R:124:6') - Reason: On CRAN
5. close to lme4 results ('test-basics.R:164:5') - Reason: On CRAN
6. basic zero inflation ('test-basics.R:217:8') - Reason: On CRAN
7. alternative binomial model specifications ('test-basics.R:236:5') - Reason: On CRAN
8. NA handling ('test-basics.R:257:5') - Reason: On CRAN
9. quine NB fit ('test-basics.R:275:5') - Reason: On CRAN
10. contrasts arg ('test-basics.R:286:5') - Reason: On CRAN
11. zero disp setting ('test-basics.R:297:5') - 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:22:5') - Reason: On CRAN
18. beta ('test-families.R:103:3') - Reason: On CRAN
19. nbinom ('test-families.R:125:5') - Reason: On CRAN
20. dbetabinom ('test-families.R:186:5') - Reason: On CRAN
21. truncated ('test-families.R:259:5') - Reason: On CRAN
22. truncated_genpois ('test-families.R:336:3') - Reason: On CRAN
23. truncated_compois ('test-families.R:352:5') - Reason: On CRAN
24. compois ('test-families.R:362:5') - Reason: On CRAN
25. genpois ('test-families.R:372:5') - Reason: On CRAN
26. tweedie ('test-families.R:380:5') - Reason: On CRAN
27. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN
28. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test
29. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN
30. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
31. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
32. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
33. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
34. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
35. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
36. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
37. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
38. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
39. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
40. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
41. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
42. two-column response ('test-predict.R:59:5') - Reason: On CRAN
43. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN
44. scale ('test-predict.R:181:5') - Reason: On CRAN
45. scale_RE ('test-predict.R:203:5') - Reason: On CRAN
46. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN
47. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN
48. contrasts carried over ('test-predict.R:291:5') - Reason: On CRAN
49. offset-only model (GH #625) ('test-predict.R:330:5') - Reason: On CRAN
50. inverse-link prediction ('test-predict.R:349:3') - Reason: On CRAN
51. nzprob doesn't segfault ('test-predict.R:440:5') - Reason: On CRAN
52. prior specs ('test-priors.R:125:5') - Reason: On CRAN
53. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test
54. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test
55. ar1 requires factor time ('test-varstruc.R:66:3') - Reason: On CRAN
56. varcorr_print ('test-varstruc.R:86:5') - Reason: On CRAN
57. cov_struct_order ('test-varstruc.R:139:5') - Reason: On CRAN
58. het ar1 ('test-varstruc.R:156:5') - Reason: On CRAN
59. zi ('test-zi.R:12:3') - Reason: On CRAN
60. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Error ('test-smooths.R:13:5'): basic smooth ──────────────────────────────
Error in ``[<-.ts`(`*tmp*`, ri, value = structure(c(1871, 1872, 1873, 1874,
1875, 1876, 1877, 1878, 1879, 1880, 1881, 1882, 1883, 1884, 1885,
1886, 1887, 1888, 1889, 1890, 1891, 1892, 1893, 1894, 1895, 1896,
1897, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907,
1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918,
1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929,
1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940,
1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951,
1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962,
1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970), tsp = c(1871,
1970, 1), class = "ts"))`: only replacement of elements is allowed
Backtrace:
▆
1. ├─testthat::expect_equal(predict(sm1), predict(sm1, newdata = ndat)) at test-smooths.R:13:5
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::predict(sm1, newdata = ndat)
5. └─glmmTMB:::predict.glmmTMB(sm1, newdata = ndat)
6. └─base::rbind(object$frame, newFr)
7. └─base::rbind(deparse.level, ...)
8. ├─base::`[<-`(`*tmp*`, ri, value = `<ts>`)
9. └─stats:::`[<-.ts`(`*tmp*`, ri, value = `<ts>`)
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.11
Check: installed package size
Result: NOTE
installed size is 97.2Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 91.3Mb
test_data 2.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.1.11
Flags: --no-vignettes
Check: installed package size
Result: NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 4.4Mb
test_data 2.7Mb
Flavor: r-oldrel-windows-x86_64