* using log directory ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/glmmTMB.Rcheck’ * using R Under development (unstable) (2025-12-17 r89188) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘glmmTMB/DESCRIPTION’ ... OK * this is package ‘glmmTMB’ version ‘1.1.13’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘glmmTMB’ can be installed ... [9m/12m] OK * used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [47s/63s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [24s/34s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘AAAtest-all.R’ [120s/149s] [121s/150s] ERROR 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) (2025-12-17 r89188) Platform: x86_64-pc-linux-gnu Running under: Fedora Linux 42 (Workstation Edition) Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.29.so; 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_1.1.13 testthat_3.3.1 loaded via a namespace (and not attached): [1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-5 [4] rlang_1.1.6 estimability_1.5.1 reformulas_0.4.3 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-15 [10] TMB_1.9.19 lme4_1.1-38 brio_1.1.5 [13] grid_4.6.0 MASS_7.3-65 mvtnorm_1.3-3 [16] lifecycle_1.0.4 numDeriv_2016.8-1.1 multcomp_1.4-29 [19] compiler_4.6.0 codetools_0.2-20 coda_0.19-4.1 [22] sandwich_3.1-1 emmeans_2.0.1 Rcpp_1.1.0.8.1 [25] mgcv_1.9-4 lattice_0.22-7 nloptr_2.2.1 [28] R6_2.6.1 Rdpack_2.6.4 splines_4.6.0 [31] rbibutils_2.4 magrittr_2.0.4 Matrix_1.7-4 [34] tools_4.6.0 boot_1.3-32 survival_3.8-3 Anova: ............... VarCorr: ............... altopt: alternative optimizers: S basics: .............SS.....S......S trickier examples: SS.SSSS............. bootMer: bootMer: SS checkRank: ................................................ control: SS..... ddf: .... diagnose: .S.. disp: ... downstream: S..... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS....................................... formulas: formula parsing: ................ mapequal: ........ mapopt: S methods: ...............................S..........................................S..............S....................................................................................... misc: . offset: SSSSSSSSS predict: .....SSSSS.................S..SSS.1..S..S...S.............S...................... priors: ...........SS propto: ...... reml: ........ rr: .......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S.............. smooths: ...... 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:218:8') - Reason: On CRAN 7. alternative binomial model specifications ('test-basics.R:237:5') - Reason: On CRAN 8. NA handling ('test-basics.R:258:5') - Reason: On CRAN 9. quine NB fit ('test-basics.R:276:5') - Reason: On CRAN 10. contrasts arg ('test-basics.R:287:5') - Reason: On CRAN 11. zero disp setting ('test-basics.R:298:5') - 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. (code run outside of `test_that()`) - Reason: empty test 28. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN 29. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test 30. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN 31. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN 32. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN 33. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN 34. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN 35. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN 36. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN 37. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN 38. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN 39. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN 40. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN 41. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN 42. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN 43. two-column response ('test-predict.R:59:5') - Reason: On CRAN 44. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN 45. scale ('test-predict.R:181:5') - Reason: On CRAN 46. scale_RE ('test-predict.R:203:5') - Reason: On CRAN 47. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN 48. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN 49. contrasts carried over ('test-predict.R:291:5') - Reason: On CRAN 50. offset-only model (GH #625) ('test-predict.R:344:5') - Reason: On CRAN 51. inverse-link prediction ('test-predict.R:363:3') - Reason: On CRAN 52. nzprob doesn't segfault ('test-predict.R:454:5') - Reason: On CRAN 53. prior specs ('test-priors.R:125:5') - Reason: On CRAN 54. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test 55. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 56. ar1 and hetar1 require factor time ('test-varstruc.R:97:3') - Reason: On CRAN 57. varcorr_print ('test-varstruc.R:124:5') - Reason: On CRAN 58. cov_struct_order ('test-varstruc.R:177:5') - Reason: On CRAN 59. basic hetar1 ('test-varstruc.R:194:5') - Reason: On CRAN 60. zi ('test-zi.R:12:3') - Reason: On CRAN 61. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-predict.R:266:5'): predvars with different ns() in fixed an Expected `predict(x, newdata = newdata)` to equal `c(1.00149139390868, 0.367732526652086, 9.21516947505197e-06)`. Differences: 1/3 mismatches [2] 0.368 - 0.368 == -2.66e-08 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [213s/364s] OK * checking PDF version of manual ... [11s/23s] OK * checking HTML version of manual ... [10s/19s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/glmmTMB.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 25:11.14, 1006.21 + 59.75