Package check result: NOTE Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Martin Elff ’ New maintainer: Martin Elff Old maintainer(s): Martin Elff Changes to worse in reverse depends: Package: projpred Check: tests New result: ERROR Running ‘testthat.R’ [107s/107s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(projpred) This is projpred version 2.9.0. > > test_check("projpred") Warning in eval(exprs, env) : On CRAN, projpred's tests based on rstanarm fits are avoided due to possible incompatibility issues between packages 'Matrix' and 'lme4' (see inline comment for this warning message). Deactivating the rstanarm tests now. Furthermore, in this case, `run_prj`, `run_vs`, and `run_cvvs` are currently set to `FALSE`. [ FAIL 4 | WARN 0 | SKIP 171 | PASS 725 ] ══ Skipped tests (171) ═════════════════════════════════════════════════════════ • !is.null(args_fit_i) is not TRUE (4): 'test_refmodel.R:82:3', 'test_refmodel.R:106:3', 'test_refmodel.R:161:3', 'test_refmodel.R:175:3' • On CRAN (7): 'test_datafit.R:608:3', 'test_div_minimizer.R:11:3', 'test_div_minimizer.R:97:3', 'test_div_minimizer.R:226:3', 'test_methods_vsel.R:715:3', 'test_misc.R:127:3', 'test_proj_predfun.R:10:3' • empty test (11): 'test_datafit.R:196:1', 'test_datafit.R:224:1', 'test_datafit.R:487:1', 'test_misc.R:7:1', 'test_misc.R:37:1', 'test_refmodel.R:5:1', 'test_refmodel.R:201:1', 'test_refmodel.R:225:1', 'test_varsel.R:36:1', 'test_varsel.R:1215:1', 'test_varsel.R:1237:1' • length(fits) > 0 is not TRUE (4): 'test_project.R:301:3', 'test_refmodel.R:214:3', 'test_refmodel.R:220:3', 'test_varsel.R:1596:3' • run_cvvs is not TRUE (39): 'test_augdat.R:437:3', 'test_augdat.R:495:3', 'test_augdat.R:565:3', 'test_datafit.R:273:3', 'test_datafit.R:555:3', 'test_methods_vsel.R:103:3', 'test_methods_vsel.R:142:3', 'test_methods_vsel.R:213:3', 'test_methods_vsel.R:264:3', 'test_methods_vsel.R:386:3', 'test_methods_vsel.R:508:3', 'test_methods_vsel.R:625:3', 'test_methods_vsel.R:652:3', 'test_methods_vsel.R:677:3', 'test_methods_vsel.R:746:3', 'test_methods_vsel.R:756:3', 'test_proj_pred.R:93:3', 'test_proj_pred.R:231:3', 'test_proj_pred.R:1166:3', 'test_proj_pred.R:1279:3', 'test_project.R:209:3', 'test_varsel.R:1179:3', 'test_varsel.R:1246:3', 'test_varsel.R:1284:3', 'test_varsel.R:1386:3', 'test_varsel.R:1413:3', 'test_varsel.R:1436:3', 'test_varsel.R:1479:3', 'test_varsel.R:1613:3', 'test_varsel.R:1726:3', 'test_varsel.R:1855:3', 'test_varsel.R:1890:3', 'test_varsel.R:2057:3', 'test_varsel.R:2125:3', 'test_varsel.R:2185:3', 'test_varsel.R:2248:3', 'test_varsel.R:2456:3', 'test_varsel.R:2555:3', 'test_varsel.R:2636:3' • run_prj is not TRUE (50): 'test_as_matrix.R:4:3', 'test_as_matrix.R:236:3', 'test_as_matrix.R:252:3', 'test_as_matrix.R:278:3', 'test_as_matrix.R:298:3', 'test_augdat.R:190:3', 'test_augdat.R:227:3', 'test_augdat.R:253:3', 'test_augdat.R:286:3', 'test_datafit.R:302:3', 'test_latent.R:65:3', 'test_latent.R:79:3', 'test_latent.R:103:3', 'test_latent.R:166:3', 'test_proj_pred.R:8:3', 'test_proj_pred.R:142:3', 'test_proj_pred.R:170:3', 'test_proj_pred.R:189:3', 'test_proj_pred.R:288:3', 'test_proj_pred.R:306:3', 'test_proj_pred.R:387:3', 'test_proj_pred.R:439:3', 'test_proj_pred.R:497:3', 'test_proj_pred.R:607:3', 'test_proj_pred.R:761:3', 'test_proj_pred.R:822:3', 'test_proj_pred.R:860:3', 'test_proj_pred.R:955:3', 'test_proj_pred.R:1004:3', 'test_proj_pred.R:1021:3', 'test_proj_pred.R:1075:3', 'test_proj_pred.R:1108:3', 'test_proj_pred.R:1200:3', 'test_proj_pred.R:1218:3', 'test_proj_pred.R:1237:3', 'test_proj_pred.R:1336:3', 'test_proj_pred.R:1356:3', 'test_proj_pred.R:1402:3', 'test_proj_pred.R:1433:3', 'test_proj_pred.R:1465:3', 'test_proj_pred.R:1564:3', 'test_proj_pred.R:1667:3', 'test_proj_pred.R:1744:3', 'test_proj_pred.R:1789:3', 'test_project.R:9:3', 'test_project.R:23:3', 'test_project.R:95:3', 'test_project.R:335:3', 'test_project.R:394:3', 'test_project.R:430:3' • run_prll is not TRUE (3): 'test_parallel.R:31:3', 'test_parallel.R:47:3', 'test_parallel.R:63:3' • run_vs is not TRUE (53): 'test_augdat.R:319:3', 'test_augdat.R:362:3', 'test_augdat.R:394:3', 'test_datafit.R:240:3', 'test_datafit.R:328:3', 'test_datafit.R:402:3', 'test_datafit.R:448:3', 'test_datafit.R:499:3', 'test_datafit.R:514:3', 'test_methods_vsel.R:41:3', 'test_methods_vsel.R:67:3', 'test_methods_vsel.R:79:3', 'test_methods_vsel.R:130:3', 'test_methods_vsel.R:154:3', 'test_methods_vsel.R:191:3', 'test_methods_vsel.R:239:3', 'test_methods_vsel.R:304:3', 'test_methods_vsel.R:450:3', 'test_methods_vsel.R:461:3', 'test_methods_vsel.R:474:3', 'test_methods_vsel.R:545:3', 'test_methods_vsel.R:556:3', 'test_methods_vsel.R:610:3', 'test_methods_vsel.R:644:3', 'test_proj_pred.R:44:3', 'test_proj_pred.R:209:3', 'test_proj_pred.R:887:3', 'test_proj_pred.R:1132:3', 'test_proj_pred.R:1257:3', 'test_proj_pred.R:1692:3', 'test_project.R:114:3', 'test_project.R:317:3', 'test_varsel.R:9:3', 'test_varsel.R:59:3', 'test_varsel.R:86:3', 'test_varsel.R:183:3', 'test_varsel.R:504:3', 'test_varsel.R:647:3', 'test_varsel.R:724:3', 'test_varsel.R:848:3', 'test_varsel.R:875:3', 'test_varsel.R:897:3', 'test_varsel.R:960:3', 'test_varsel.R:1033:3', 'test_varsel.R:1048:3', 'test_varsel.R:1063:3', 'test_varsel.R:1074:3', 'test_varsel.R:1087:3', 'test_varsel.R:1124:3', 'test_varsel.R:1945:3', 'test_varsel.R:1997:3', 'test_varsel.R:2314:3', 'test_varsel.R:2379:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_proj_predfun.R:419:3'): repair_re() works for multilevel categorical() models with only a single group variable ── `... <- NULL` produced unexpected warnings. Expected match: Inner iterations did not coverge Actual values: * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) ── Error ('test_proj_predfun.R:455:5'): repair_re() works for multilevel categorical() models with only a single group variable ── Error in `eval(substitute(object$call$catCov))`: object 'mfit' not found Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_proj_predfun.R:455:5 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─stats::predict(mfit, newdata = VA_new_dummy) 7. └─mclogit:::predict.mmblogit(mfit, newdata = VA_new_dummy) ── Failure ('test_proj_predfun.R:661:3'): repair_re() works for multilevel categorical() models with multiple group variables ── `... <- NULL` produced unexpected warnings. Expected match: Inner iterations did not coverge Actual values: * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) * Possible non-convergence of inner iterations - nlminb message: false convergence (8) ── Error ('test_proj_predfun.R:698:5'): repair_re() works for multilevel categorical() models with multiple group variables ── Error in `eval(substitute(object$call$catCov))`: object 'mfit' not found Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_proj_predfun.R:698:5 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─stats::predict(mfit, newdata = VA_new_dummy) 7. └─mclogit:::predict.mmblogit(mfit, newdata = VA_new_dummy) [ FAIL 4 | WARN 0 | SKIP 171 | PASS 725 ] Error: Test failures Execution halted Package: vecmatch Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [22s/22s] 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(vecmatch) > > test_check("vecmatch") Failed with error: 'unused argument (quitely = TRUE)' Failed with error: 'unused argument (quitely = TRUE)' Failed with error: 'unused argument (quitely = TRUE)' Failed with error: 'unused argument (quitely = TRUE)' Failed with error: 'unused argument (quitely = TRUE)' [ FAIL 4 | WARN 4 | SKIP 1 | PASS 243 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-optimize_gps.R:187:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-estimate_gps.R:202:3'): estimate_gps: methods and scenarios ── Expected `estimate_gps(treat ~ pred, data, method = "mblogit")` to run without any errors. i Actually got a with text: There was a problem fitting the baseline_category_logit regressions with `mclogit::mblogit. Error message: (from `mclogit::mblogit`) object 'dispersion' not found ── Failure ('test-estimate_gps_multinom.R:129:3'): Checking `mclogit` method ─── Expected `estimate_gps(treat ~ pred, data, method = "mblogit")` to run without any errors. i Actually got a with text: There was a problem fitting the baseline_category_logit regressions with `mclogit::mblogit. Error message: (from `mclogit::mblogit`) object 'dispersion' not found ── Failure ('test-estimate_gps_multinom.R:132:3'): Checking `mclogit` method ─── Expected `estimate_gps(treat ~ pred, data, method = "mblogit", link = "baseline_category_logit")` to run without any errors. i Actually got a with text: There was a problem fitting the baseline_category_logit regressions with `mclogit::mblogit. Error message: (from `mclogit::mblogit`) object 'dispersion' not found ── Failure ('test-estimate_gps_multinom.R:148:3'): Checking `mclogit` method ─── Expected `estimate_gps(treat ~ pred, data, method = "mblogit", control = mclogit::mclogit.control(maxit = 30))` to run without any errors. i Actually got a with text: There was a problem fitting the baseline_category_logit regressions with `mclogit::mblogit. Error message: (from `mclogit::mblogit`) object 'dispersion' not found [ FAIL 4 | WARN 4 | SKIP 1 | PASS 243 ] Error: Test failures Execution halted