* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/badp.Rcheck’ * using R Under development (unstable) (2026-03-11 r89605) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-03-12 09:39:17 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘badp/DESCRIPTION’ ... OK * this is package ‘badp’ version ‘0.4.0’ * 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 ‘badp’ can be installed ... [82s/90s] OK * used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ * 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 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 ... [18s/27s] 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 pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [66s/73s] [66s/74s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(badp) > > test_check("badp") The number of the best models (top) cannot be higher than the total number of models. We set top = R (total number of regressors) and continiue :) Saving _problems/test-model_space-66.R [ FAIL 1 | WARN 6 | SKIP 5 | PASS 89 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • On CRAN (5): 'test-SEM_likelihood.R:13:3', 'test-SEM_likelihood.R:27:3', 'test-SEM_likelihood.R:42:3', 'test-SEM_likelihood.R:58:3', 'test-model_space.R:156:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-model_space.R:66:3'): optim_model_space_params correctly computes small_economic_growth_ms ── Discrepancies between matrices exceed given tolerances. - FALSE represents a mismatch - NA is ok (it was checked that they are in the same place) Discrepancies at: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] alpha TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE phi_0 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE err_var TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE dep_var_1 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE dep_var_2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE dep_var_3 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE dep_var_4 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE beta_ish NA TRUE NA TRUE NA TRUE NA TRUE beta_sed NA NA TRUE TRUE NA NA TRUE TRUE beta_pgrw NA NA NA NA TRUE TRUE FALSE TRUE phi_1_ish NA TRUE NA TRUE NA TRUE NA TRUE phi_1_sed NA NA TRUE TRUE NA NA TRUE TRUE phi_1_pgrw NA NA NA NA TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE Expected: [,1] [,2] [,3] [,4] [,5] alpha 1.0745814406 1.028340940 1.1289131964 1.091650e+00 1.057320e+00 phi_0 -0.0656645084 -0.049787969 -0.1377595121 -1.212341e-01 -7.322008e-02 err_var 0.0842404238 0.053596906 0.0689079995 3.106891e-02 7.342810e-02 dep_var_1 0.1982081508 0.166210936 0.1972420072 1.692213e-01 1.933317e-01 dep_var_2 0.1755113818 0.181340091 0.1810585639 1.883098e-01 1.762445e-01 dep_var_3 0.1782033084 0.180041826 0.1819531858 1.839022e-01 1.772040e-01 dep_var_4 0.1605445583 0.160702848 0.1685759224 1.697835e-01 1.595198e-01 beta_ish NA 0.118782652 NA 1.200653e-01 NA beta_sed NA NA -0.0724277353 -6.043068e-02 NA beta_pgrw NA NA NA NA -9.770270e-03 phi_1_ish NA -0.030215605 NA -3.543411e-02 NA phi_1_sed NA NA 0.1312014964 9.742165e-02 NA phi_1_pgrw NA NA NA NA -4.703498e-02 0.0354665352 -0.005744763 0.0278520957 -7.600020e-03 2.856839e-02 0.0245291751 0.019259807 0.0078029236 7.437451e-03 1.762154e-02 -0.0454170637 -0.038335492 -0.0360590046 -3.212170e-02 -1.965637e-02 0.0534096865 0.004407241 0.0463234773 -2.199226e-03 4.778356e-02 0.0270377067 0.019411734 0.0121198279 9.654390e-03 1.733184e-02 -0.0550849946 -0.050237419 -0.0444491957 -4.190557e-02 -2.853898e-02 0.0535232474 -0.001697534 0.0422249091 -1.223920e-02 4.877887e-02 0.0436052972 0.029740978 0.0359300870 2.557554e-02 3.280566e-02 -0.0540059134 -0.045992273 -0.0452227023 -3.953640e-02 -2.525268e-02 0.0726722695 -0.005454683 0.0717170724 -3.479021e-03 6.696547e-02 0.0041506485 -0.011741307 0.0064089907 -2.414291e-03 5.027479e-04 -0.0127473142 0.012551672 -0.0121455993 8.682047e-03 2.409429e-03 0.0278015654 0.017821355 0.0272599777 2.306718e-02 2.385125e-02 0.0151656731 -0.005026662 0.0137787601 2.417239e-03 9.583390e-03 -0.0051511929 0.014720292 -0.0059506695 9.470971e-03 9.432142e-03 0.0327125576 0.034535595 0.0348815535 4.297769e-02 3.025404e-02 0.0159516977 -0.008670639 0.0095595180 -6.502804e-03 9.892125e-03 -0.0177580975 0.005369407 -0.0179866913 1.498431e-03 -3.113474e-03 -0.0005656614 0.027501378 -0.0008474924 3.042014e-02 -1.611139e-03 0.0089235231 0.007638269 0.0037471265 2.608508e-03 8.982765e-03 0.0016465889 0.006993300 0.0014388460 5.695225e-03 1.296084e-03 0.0004534685 0.039216651 0.0025723263 4.495182e-02 7.786751e-05 0.0058224602 0.007717787 -0.0027017927 8.064999e-05 5.966808e-03 -0.0049067563 0.005132485 -0.0057672716 4.201455e-03 -6.482804e-03 0.0181005129 0.034788470 0.0200952090 3.635872e-02 1.799205e-02 -0.0096251444 -0.010183986 -0.0148641185 -1.416711e-02 -9.813481e-03 0.0172003224 0.016920640 0.0154281072 1.567370e-02 1.466855e-02 [,6] [,7] [,8] alpha 1.018223082 1.133017175 1.085189e+00 phi_0 -0.056696656 -0.152758082 -1.231308e-01 err_var 0.041947725 0.050998203 7.648379e-04 dep_var_1 0.164988678 0.193204937 1.675544e-01 dep_var_2 0.180341851 0.185372369 1.884733e-01 dep_var_3 0.178501532 0.182842827 1.820396e-01 dep_var_4 0.159159728 0.169142329 1.676652e-01 beta_ish 0.116255906 NA 1.169100e-01 beta_sed NA -0.087994419 -7.200476e-02 beta_pgrw -0.010010374 -0.027560350 -2.463021e-02 phi_1_ish -0.035055645 NA -3.773487e-02 phi_1_sed NA 0.123307102 9.258983e-02 phi_1_pgrw -0.034895104 -0.025843672 -1.889879e-02 -0.005671510 0.021142471 -7.484152e-03 0.014636237 0.007308161 7.425179e-03 -0.018914718 -0.016114559 -1.698421e-02 0.002544823 0.041472338 -2.086269e-03 0.012722816 0.010870116 9.233276e-03 -0.029296288 -0.020912372 -2.333378e-02 -0.002086713 0.036493272 -1.138338e-02 0.023047510 0.032784330 2.476098e-02 -0.021664745 -0.015944792 -1.492122e-02 -0.006227388 0.067263298 -4.327416e-03 -0.012419712 0.005462894 -2.891286e-03 0.015954305 0.001346896 1.381102e-02 0.015424458 0.024107468 1.956733e-02 -0.006139629 0.010775417 7.721782e-04 0.017512053 0.005195717 1.262688e-02 0.031853472 0.034955962 4.008648e-02 -0.010398951 0.004904905 -9.510640e-03 0.005559271 -0.009269175 5.586428e-05 0.025430301 -0.001420808 2.746091e-02 0.007776261 0.002727356 1.938433e-03 0.004878535 -0.002699096 9.445058e-04 0.036067125 0.004292555 4.157759e-02 0.006765355 -0.004375529 -2.277850e-03 -0.001399854 -0.015264143 -8.327731e-03 0.033423731 0.021025622 3.500575e-02 -0.010718830 -0.016236653 -1.530213e-02 0.012019008 0.007420493 6.692401e-03 Actual: [,1] [,2] [,3] [,4] [,5] alpha 1.0745814427 1.028340946 1.1289131964 1.091650e+00 1.057320e+00 phi_0 -0.0656645104 -0.049787974 -0.1377595113 -1.212341e-01 -7.322008e-02 err_var 0.0842404233 0.053596905 0.0689079998 3.106900e-02 7.342810e-02 dep_var_1 0.1982081509 0.166210936 0.1972420092 1.692213e-01 1.933317e-01 dep_var_2 0.1755113818 0.181340092 0.1810585631 1.883096e-01 1.762445e-01 dep_var_3 0.1782033090 0.180041825 0.1819531864 1.839022e-01 1.772040e-01 dep_var_4 0.1605445586 0.160702849 0.1685759216 1.697834e-01 1.595198e-01 beta_ish NA 0.118782651 NA 1.200650e-01 NA beta_sed NA NA -0.0724277360 -6.043072e-02 NA beta_pgrw NA NA NA NA -9.770268e-03 phi_1_ish NA -0.030215605 NA -3.543389e-02 NA phi_1_sed NA NA 0.1312014962 9.742173e-02 NA phi_1_pgrw NA NA NA NA -4.703498e-02 0.0354665344 -0.005744763 0.0278520962 -7.599961e-03 2.856839e-02 0.0245291752 0.019259807 0.0078029236 7.437448e-03 1.762154e-02 -0.0454170636 -0.038335491 -0.0360590048 -3.212168e-02 -1.965637e-02 0.0534096862 0.004407242 0.0463234775 -2.199091e-03 4.778356e-02 0.0270377067 0.019411734 0.0121198278 9.654398e-03 1.733184e-02 -0.0550849943 -0.050237418 -0.0444491957 -4.190560e-02 -2.853898e-02 0.0535232468 -0.001697533 0.0422249091 -1.223904e-02 4.877887e-02 0.0436052973 0.029740979 0.0359300868 2.557556e-02 3.280566e-02 -0.0540059129 -0.045992273 -0.0452227024 -3.953636e-02 -2.525268e-02 0.0726722698 -0.005454683 0.0717170702 -3.479142e-03 6.696547e-02 0.0041506487 -0.011741306 0.0064089914 -2.414299e-03 5.027479e-04 -0.0127473143 0.012551671 -0.0121455992 8.682034e-03 2.409429e-03 0.0278015654 0.017821355 0.0272599785 2.306698e-02 2.385125e-02 0.0151656734 -0.005026662 0.0137787616 2.417194e-03 9.583390e-03 -0.0051511933 0.014720291 -0.0059506692 9.470994e-03 9.432143e-03 0.0327125581 0.034535595 0.0348815549 4.297751e-02 3.025404e-02 0.0159516979 -0.008670639 0.0095595199 -6.502870e-03 9.892125e-03 -0.0177580976 0.005369408 -0.0179866902 1.498400e-03 -3.113473e-03 -0.0005656619 0.027501377 -0.0008474931 3.041997e-02 -1.611138e-03 0.0089235230 0.007638268 0.0037471267 2.608497e-03 8.982765e-03 0.0016465882 0.006993299 0.0014388449 5.695379e-03 1.296084e-03 0.0004534687 0.039216651 0.0025723262 4.495161e-02 7.786773e-05 0.0058224599 0.007717786 -0.0027017925 8.062467e-05 5.966808e-03 -0.0049067561 0.005132486 -0.0057672725 4.201481e-03 -6.482803e-03 0.0181005136 0.034788471 0.0200952096 3.635871e-02 1.799205e-02 -0.0096251446 -0.010183987 -0.0148641182 -1.416711e-02 -9.813481e-03 0.0172003220 0.016920639 0.0154281070 1.567364e-02 1.466855e-02 [,6] [,7] [,8] alpha 1.018222944 1.132316671 1.085189e+00 phi_0 -0.056696510 -0.152010848 -1.231306e-01 err_var 0.041947798 0.051609192 7.646068e-04 dep_var_1 0.164988653 0.193240009 1.675544e-01 dep_var_2 0.180341812 0.185359009 1.884732e-01 dep_var_3 0.178501495 0.182791522 1.820396e-01 dep_var_4 0.159159741 0.169089327 1.676652e-01 beta_ish 0.116255900 NA 1.169101e-01 beta_sed NA -0.088004494 -7.200458e-02 beta_pgrw -0.010010338 -0.026532884 -2.463018e-02 phi_1_ish -0.035055647 NA -3.773489e-02 phi_1_sed NA 0.123678848 9.258969e-02 phi_1_pgrw -0.034895163 -0.026726319 -1.889881e-02 -0.005671506 0.021246563 -7.484156e-03 0.014636238 0.007355497 7.425172e-03 -0.018914719 -0.016262350 -1.698421e-02 0.002544828 0.041560651 -2.086278e-03 0.012722819 0.010994520 9.233250e-03 -0.029296300 -0.021108903 -2.333380e-02 -0.002086706 0.036675615 -1.138338e-02 0.023047526 0.032979136 2.476095e-02 -0.021664765 -0.016401893 -1.492123e-02 -0.006227393 0.067229669 -4.327428e-03 -0.012419704 0.005460127 -2.891275e-03 0.015954302 0.001457422 1.381102e-02 0.015424454 0.024105536 1.956733e-02 -0.006139624 0.010754224 7.722067e-04 0.017512058 0.005312972 1.262690e-02 0.031853463 0.034881833 4.008648e-02 -0.010398957 0.004842325 -9.510601e-03 0.005559308 -0.008783874 5.587111e-05 0.025430306 -0.001446198 2.746094e-02 0.007776254 0.002639334 1.938455e-03 0.004878563 -0.002637082 9.445377e-04 0.036067124 0.004181640 4.157761e-02 0.006765334 -0.004502432 -2.277810e-03 -0.001399882 -0.014761974 -8.327710e-03 0.033423730 0.020969228 3.500576e-02 -0.010718840 -0.016248153 -1.530212e-02 0.012019045 0.007798542 6.692396e-03 [ FAIL 1 | WARN 6 | SKIP 5 | PASS 89 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [79s/110s] OK * checking PDF version of manual ... [8s/12s] OK * checking HTML version of manual ... 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-ATLAS/badp.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:38.05, 295.56 + 17.44