Your message dated Fri, 25 Aug 2023 13:04:41 +0000 with message-id <[email protected]> and subject line Bug#1039650: fixed in r-cran-glmmtmb 1.1.7+dfsg-2 has caused the Debian Bug report #1039650, regarding r-cran-glmmtmb: autopkgtest failure with r-base (4.3.1-1) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 1039650: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1039650 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: r-cran-glmmtmb Version: 1.1.5+dfsg-4 Severity: serious Justification: autopkgtest failure Dear Maintainer, The autopkgtest of your package fails with r-base (4.3.1-1): 50s autopkgtest [01:19:09]: test run-unit-test: [----------------------- 50s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 50s BEGIN TEST AAAtest-all.R 50s 50s R version 4.3.1 (2023-06-16) -- "Beagle Scouts" 50s Copyright (C) 2023 The R Foundation for Statistical Computing 50s Platform: x86_64-pc-linux-gnu (64-bit) 50s 50s R is free software and comes with ABSOLUTELY NO WARRANTY. 50s You are welcome to redistribute it under certain conditions. 50s Type 'license()' or 'licence()' for distribution details. 50s 50s R is a collaborative project with many contributors. 50s Type 'contributors()' for more information and 50s 'citation()' on how to cite R or R packages in publications. 50s 50s Type 'demo()' for some demos, 'help()' for on-line help, or 50s 'help.start()' for an HTML browser interface to help. 50s Type 'q()' to quit R. 50s 50s > if (require("testthat")) { 50s + pkg <- "glmmTMB" 50s + require(pkg, character.only=TRUE) 50s + print(sessionInfo()) 50s + test_check(pkg, reporter="summary") 50s + print(warnings()) # TODO? catch most of these by expect_warning(..) 50s + } else { 50s + warnings("Package 'testthat' not available, cannot run unit tests for package", 50s + sQuote(pkg)) 50s + } 50s Loading required package: testthat 51s Loading required package: glmmTMB 52s R version 4.3.1 (2023-06-16) 52s Platform: x86_64-pc-linux-gnu (64-bit) 52s Running under: Debian GNU/Linux trixie/sid 52s 52s Matrix products: default 52s BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 52s LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 52s 52s locale: 52s [1] C 52s 52s time zone: Etc/UTC 52s tzcode source: system (glibc) 52s 52s attached base packages: 52s [1] stats graphics grDevices utils datasets methods base 52s 52s other attached packages: 52s [1] glmmTMB_1.1.5 testthat_3.1.6 52s 52s loaded via a namespace (and not attached): 52s [1] nlme_3.1-162 cli_3.6.0 rlang_1.0.6 52s [4] TH.data_1.1-1 estimability_1.4.1 xtable_1.8-4 52s [7] minqa_1.2.5 zoo_1.8-11 TMB_1.9.2 52s [10] lme4_1.1-31 brio_1.1.3 grid_4.3.1 52s [13] MASS_7.3-60 mvtnorm_1.1-3 numDeriv_2016.8-1.1 52s [16] compiler_4.3.1 multcomp_1.4-22 codetools_0.2-19 52s [19] sandwich_3.0-2 emmeans_1.8.4-1 coda_0.19-4 52s [22] Rcpp_1.0.10 lattice_0.20-45 nloptr_2.0.3 52s [25] R6_2.5.1 splines_4.3.1 magrittr_2.0.3 52s [28] Matrix_1.5-3 boot_1.3-28.1 survival_3.5-3 53s Anova: .............. 56s VarCorr: ............. 56s altopt: 56s alternative optimizers: S 58s basics: .............SS.....S12..3.S 59s trickier examples: SS.SSSS...... 59s bootMer: 59s bootMer: SS 65s checkRank: ..................................W......W.. 65s control: SS 65s diagnose: . 67s disp: ... 68s downstream: S.. 68s edgecases: 68s test edge cases: . 68s env: 70s basic examples: ... 70s families: 71s alternative binomial specifications: .......... 73s non-integer count warnings: ....... 73s fitting exotic families: SSSSS 73s trunc compois: S 73s compois: S 73s genpois: S 73s tweedie: S. 73s link function info available: ............ 74s link info added to family: ...... 74s formulas: 74s formula parsing: ................ 74s mapopt: 79s methods: ............................S.................................................... 79s simulate consistency with glm/lm: ... 82s Ranef etc.: .......S........... 83s misc: . 83s offset: SSSSSSSSS 83s predict: .....SSS 88s Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W.. 88s reml: 89s REML: ....... 89s rr: W 89s saveload: 90s Saving and loading glmmTMB objects: . 90s sparseX: 90s sparse X models: ....... 90s start: .. 90s utils: .............. 90s varstruc: 90s variance structures: ........SSS 91s weight: ......... 91s zi: 91s ZI models: SS 91s 91s == Skipped ===================================================================== 91s 1. downstream methods work with optim() ('test-altopt.R:11') - Reason: On CRAN 91s 91s 2. Update Gaussian ('test-basics.R:68') - Reason: On CRAN 91s 91s 3. Variance structures ('test-basics.R:77') - Reason: On CRAN 91s 91s 4. Multiple RE, reordering ('test-basics.R:107') - Reason: On CRAN 91s 91s 5. close to lme4 results ('test-basics.R:142') - Reason: On CRAN 91s 91s 6. basic zero inflation ('test-basics.R:195') - Reason: On CRAN 91s 91s 7. alternative binomial model specifications ('test-basics.R:213') - Reason: On CRAN 91s 91s 8. NA handling ('test-basics.R:234') - Reason: On CRAN 91s 91s 9. quine NB fit ('test-basics.R:252') - Reason: On CRAN 91s 91s 10. contrasts arg ('test-basics.R:263') - Reason: On CRAN 91s 91s 11. zero disp setting ('test-basics.R:274') - Reason: On CRAN 91s 91s 12. Bernoulli responses ('test-bootMer.R:12') - Reason: On CRAN 91s 91s 13. binomial responses ('test-bootMer.R:22') - Reason: On CRAN 91s 91s 14. profile method ('test-control.R:16') - Reason: On CRAN 91s 91s 15. parallel regions ('test-control.R:50') - Reason: On CRAN 91s 91s 16. emmeans ('test-downstream.R:8') - Reason: On CRAN 91s 91s 17. beta ('test-families.R:90') - Reason: On CRAN 91s 91s 18. nbinom ('test-families.R:112') - Reason: On CRAN 91s 91s 19. dbetabinom ('test-families.R:167') - Reason: On CRAN 91s 91s 20. truncated ('test-families.R:240') - Reason: On CRAN 91s 91s 21. truncated_genpois ('test-families.R:317') - Reason: On CRAN 91s 91s 22. truncated_compois ('test-families.R:334') - Reason: On CRAN 91s 91s 23. compois ('test-families.R:345') - Reason: On CRAN 91s 91s 24. genpois ('test-families.R:356') - Reason: On CRAN 91s 91s 25. tweedie ('test-families.R:365') - Reason: On CRAN 91s 91s 26. anova ML/REML checks ('test-methods.R:117') - Reason: On CRAN 91s 91s 27. various binomial response types work ('test-methods.R:478') - Reason: On CRAN 91s 91s 28. LM with offset as argument ('test-offset.R:27') - Reason: On CRAN 91s 91s 29. LM with offset in formula ('test-offset.R:35') - Reason: On CRAN 91s 91s 30. LM with offset in formula - variable not in environment ('test-offset.R:48') - Reason: On CRAN 91s 91s 31. LM with offset in dispersion formula ('test-offset.R:57') - Reason: On CRAN 91s 91s 32. LM with multiple offsets (cond/dispersion) ('test-offset.R:65') - Reason: On CRAN 91s 91s 33. LM with random crap in the formula ('test-offset.R:74') - Reason: On CRAN 91s 91s 34. offset in do.call ('test-offset.R:81') - Reason: On CRAN 91s 91s 35. LONG offset in do.call ('test-offset.R:90') - Reason: On CRAN 91s 91s 36. offset works with attributes ('test-offset.R:101') - Reason: On CRAN 91s 91s 37. new levels of fixed effect factor ('test-predict.R:37') - Reason: On CRAN 91s 91s 38. new levels in RE term ('test-predict.R:44') - Reason: On CRAN 91s 91s 39. new levels in AR1 (OK) ('test-predict.R:51') - Reason: On CRAN 91s 91s 40. two-column response ('test-predict.R:61') - Reason: On CRAN 91s 91s 41. Prediction with dispformula=~0 ('test-predict.R:69') - Reason: On CRAN 91s 91s 42. scale ('test-predict.R:183') - Reason: On CRAN 91s 91s 43. scale_RE ('test-predict.R:205') - Reason: On CRAN 91s 91s 44. complex bases in dispformula ('test-predict.R:212') - Reason: On CRAN 91s 91s 45. fix_predvars works for I(x^2) ('test-predict.R:224') - Reason: On CRAN 91s 91s 46. contrasts carried over ('test-predict.R:285') - Reason: On CRAN 91s 91s 47. offset-only model (GH #625) ('test-predict.R:324') - Reason: On CRAN 91s 91s 48. inverse-link prediction ('test-predict.R:343') - Reason: On CRAN 91s 91s 49. nzprob doesn't segfault ('test-predict.R:434') - Reason: On CRAN 91s 91s 50. ar1 requires factor time ('test-varstruc.R:52') - Reason: On CRAN 91s 91s 51. varcorr_print ('test-varstruc.R:72') - Reason: On CRAN 91s 91s 52. cov_struct_order ('test-varstruc.R:103') - Reason: On CRAN 91s 91s 53. zi ('test-zi.R:12') - Reason: On CRAN 91s 91s 54. zi beta and Gamma ('test-zi.R:37') - Reason: On CRAN 91s 91s == Warnings ==================================================================== 91s 1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting') 91s 91s 2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting') 91s 91s 3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting') 91s 91s 4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting') 91s 91s 5. (code run outside of `test_that()`) ('test-rr.R:9') - there is no package called 'mvabund' 91s 91s == Failed ====================================================================== 91s -- 1. Failure ('test-basics.R:120'): Alternative family specifications [via upda 91s `gm0` not equal to `res_chr`. 91s Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components 91s 91s -- 2. Failure ('test-basics.R:121'): Alternative family specifications [via upda 91s `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE). 91s Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components 91s 91s -- 3. Failure ('test-basics.R:132'): Update Binomial --------------------------- 91s `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE). 91s Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components 91s 91s == DONE ======================================================================== 91s Error: Test failures https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-glmmtmb/34918480/log.gz
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--- Begin Message ---Source: r-cran-glmmtmb Source-Version: 1.1.7+dfsg-2 Done: Andreas Tille <[email protected]> We believe that the bug you reported is fixed in the latest version of r-cran-glmmtmb, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated r-cran-glmmtmb package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 25 Aug 2023 14:38:04 +0200 Source: r-cran-glmmtmb Architecture: source Version: 1.1.7+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <[email protected]> Changed-By: Andreas Tille <[email protected]> Closes: 1039650 Changes: r-cran-glmmtmb (1.1.7+dfsg-2) unstable; urgency=medium . * Rebuild against latest R and latest r-cran-tmb Closes: #1039650 * Semi-manually update debian/tests/control since dh-update-R does not work with two separate test sections Checksums-Sha1: 928846237074799493cfc277e18c77bae717c4d0 2560 r-cran-glmmtmb_1.1.7+dfsg-2.dsc a62e89d561cdf73558b2d92c281e404709c5cb91 14732 r-cran-glmmtmb_1.1.7+dfsg-2.debian.tar.xz 70295930c4efc305e8fa7b18ba46db0f7741958b 12130 r-cran-glmmtmb_1.1.7+dfsg-2_amd64.buildinfo Checksums-Sha256: 379df1c0950d64016ef2b5d72b9aa95fa9d5ea316a70db680d61d0d86966454e 2560 r-cran-glmmtmb_1.1.7+dfsg-2.dsc 7750608befd03b16ef07e8d9b8490663f6ac46e946d73a88ced0aa18200e5c6f 14732 r-cran-glmmtmb_1.1.7+dfsg-2.debian.tar.xz 0576b8c900bedd38b9cabb762db6cdeb8c807170e9d3d8e783397f40445225e5 12130 r-cran-glmmtmb_1.1.7+dfsg-2_amd64.buildinfo Files: d01fbab7e0edfb1df01ba8ad86ab03e5 2560 gnu-r optional r-cran-glmmtmb_1.1.7+dfsg-2.dsc 0d567db6e3b255c3fc06ddec62840e01 14732 gnu-r optional r-cran-glmmtmb_1.1.7+dfsg-2.debian.tar.xz d8309fb9b71c694dbbe831ffde41b3ed 12130 gnu-r optional r-cran-glmmtmb_1.1.7+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmToofkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHMHg/+PgJbkS10ijW7uOczLtC/mdRN5rhSOhEE bHiUcNfJzqIdzTTc3fGfED/V3TgrjUv/PjlbLyLngPYInDOuUffVt/VMW0NXG8ys LAJo8Y9rtGFCB3bP2YwL4szyVj0aDwFV8KNK/2MIxlGrxyUyINxYsFrkdlObWSdH TzxFFGgHb0/cMf/6s5rNJpniQVpRjNcFq7+G0DFT36s09Ed+gbiEo1ew89EvT0VF 9UrThTiX6yL7b7saPajDtH7I+JsD49RIfDSsDQ7ycTXr2Nja/MAk9JFGL7JyA93h BZJvRBhBk6w6aSpBsTwL8n6/BK2tQhC8v5k9oU9tcoG8kMlE1rBESpl40TCyZG0N ARuKNLA95Vo+dsA0OGAVv22cAFJQg5gOQEHGYo+XW3FzWEMEcFHeOKdQK3az4M6p 6GeTtrOMQdGEfAqxR2Z4yWd+z3UDPQR/FM0uobH1RzZjQSQHJGd1E67SMEjzJYC0 bp135OTiLtu10AXGdBcl8I6fH18BUWzKB2kdvG3hQI0khX9i7CakNQCHD9uIc0GN hxknYHy2DOUqqYBsmG//xSyTGChcE+l848CEZA1nXfzXpC7DvT4hSneyJ9Wh/cn0 l9MTOHf/OhSueTsUmtb5FQi/6Yh3aQK9vjynrCQtVhJMda8huP1IY+zboYJg2Laq mPeF3NtpbzQ= =Wvq4 -----END PGP SIGNATURE-----
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