• using R Under development (unstable) (2025-03-29 r88074)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3)     Debian flang-new version 19.1.7 (3)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘glmmTMB/DESCRIPTION’ ... OK
• this is package ‘glmmTMB’ version ‘1.1.10’
• 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 ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 19.1.7 (3)’
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘methods.R’
• 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 ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [2s/3s] OK
• checking whether startup messages can be suppressed ... [3s/3s] 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 ... [28s/36s] OK
• checking Rd files ... [1s/1s] 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 ... [0s/1s] 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
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• 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 ... [14s/17s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [107s/127s] ERROR   Running ‘AAAtest-all.R’ [107s/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) (2025-03-29 r88074)   Platform: x86_64-pc-linux-gnu   Running under: Debian GNU/Linux trixie/sid      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_1.1.10 testthat_3.2.3      loaded via a namespace (and not attached):    [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3    [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0    [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13   [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_1.11.0   [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1   [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1   [28] Rdpack_2.6.3 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: S1....   edgecases:   test edge cases: .   env:   basic examples: ...   families: .....................SSSSSSSSS..................................   formulas:   formula parsing: ................   mapequal: ........   mapopt:   methods: ...............................S..........................................S..............S.......................   misc: .   offset: SSSSSSSSS   predict: .....SSS   Predict two-column response case: SS.................S..SSS....S..S...S.............S.......   priors: ...........S   propto: .....   reml: ........   rr: .........   saveload:   Saving and loading glmmTMB objects: .   simulate: .........   simulate_new: ....S.........   smooths: ......   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: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:61:5') - Reason: On CRAN      43. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN      44. scale ('test-predict.R:183:5') - Reason: On CRAN      45. scale_RE ('test-predict.R:205:5') - Reason: On CRAN      46. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN      47. fix_predvars works for I(x^2) ('test-predict.R:225:5') - Reason: On CRAN      48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN      49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN      50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN      51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN      52. prior specs ('test-priors.R:125:5') - Reason: On CRAN      53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test      54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN      55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN      56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN      57. zi ('test-zi.R:12:3') - Reason: On CRAN      58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN      ══ Failed ══════════════════════════════════════════════════════════════════════   ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ──   c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))).   Component "p.value": Mean relative difference: 1.553134e-05      ══ DONE ════════════════════════════════════════════════════════════════════════   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [107s/138s] OK
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [3s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE