* using log directory 'd:/RCompile/CRANincoming/R-devel/surveymixr.Rcheck' * using R Under development (unstable) (2025-11-20 r89043 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'surveymixr/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'surveymixr' version '0.2.1' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Siyang Ni ' New submission Possibly misspelled words in DESCRIPTION: Asparouhov (23:50) BLRT (15:38) ECLS (21:48) GMM (11:50) LMR (15:68) Mendell (15:48) Mplus (22:43) NLSY (21:42) Vermunt (24:45) * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'surveymixr' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: 'TEST_COVERAGE_QUICK_REFERENCE.txt' 'TROUBLESHOOTING.md' * 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 ... [13s] 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [526s] ERROR Running 'testthat.R' [526s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(surveymixr) > > test_check("surveymixr") Growth Mixture Model with 2 Classes ===================================== Model: Growth model: linear N = 100 individuals T = 4 time points Parameters: 7 Survey Design: Weights: No Clustering: No Stratification: No Fit: LogLik: -1012.04 AIC: 2038.08 BIC: 2056.32 Entropy: 0.000 Class Proportions (Weighted): Class 1: 0.493 Class 2: 0.507 Convergence: Status: Converged Iterations: 5 Random starts: 10 Best solution replicated: 1 times --- Use summary() for detailed results Use plot() to visualize trajectories ======================================== Growth Mixture Model - Detailed Summary ======================================== MODEL SPECIFICATION ------------------- Growth model: linear Number of classes: 2 Sample size: 100 Time points: 4 Time scores: 0, 1, 2, 3 SURVEY DESIGN ------------- Sampling weights: No GROWTH PARAMETERS ----------------- Class 1 (n = 0.0, 49.3%): Intercept: 9.573 (SE = 1.000) Slope: -0.330 (SE = 1.000) Residual SD: 4.018 (SE = 0.338) Class 2 (n = 100.0, 50.7%): Intercept: 9.573 (SE = 1.000) Slope: -0.330 (SE = 1.000) Residual SD: 4.030 (SE = 0.337) CLASS PROPORTIONS ----------------- Class Weighted Unweighted 1 0.493 0.493 2 0.507 0.507 FIT INDICES ----------- Log-likelihood: -1012.04 Parameters: 7 AIC: 2038.08 BIC: 2056.32 aBIC: 2034.21 Entropy: 0.000 Average posterior prob: 0.507 CLASSIFICATION QUALITY ---------------------- Class AvePP OCC 1 NA NA 2 0.507 1.03 CONVERGENCE ----------- Status: Converged Iterations: 5 Random starts: 10 Best logLik: -1012.04 Replications: 1 WARNING: Best solution not replicated. Consider increasing 'starts'. Computation time: 0.7 seconds ======================================== n_classes loglik aic bic abic entropy smallest_class 1 1 -2411.522 4829.043 4839.608 4830.097 NaN 1.000 2 2 -2320.153 4654.306 4678.956 4656.766 0.7187677 0.152 3 3 -2320.153 4662.306 4701.042 4666.171 0.3265901 0.164 4 4 -2320.153 4670.306 4723.128 4675.577 0.2319569 0.184 n_params converged 1 3 TRUE 2 7 TRUE 3 11 TRUE 4 15 TRUE n_classes loglik aic bic abic entropy smallest_class 1 2 -2340.698 4695.396 4720.046 4697.856 0.7191759 0.164 2 3 -2340.585 4703.171 4741.907 4707.036 0.3225037 0.208 n_params converged 1 7 TRUE 2 11 TRUE n_classes loglik aic bic abic entropy smallest_class 1 1 -1959.571 3925.142 3935.037 3925.533 NaN 1.00 2 2 -1940.960 3895.920 3919.008 3896.831 0.3692386 0.32 3 3 -1940.960 3903.921 3940.202 3905.353 0.4140324 0.31 n_params converged 1 3 TRUE 2 7 TRUE 3 11 TRUE n_classes loglik aic bic abic entropy smallest_class 1 2 -3550.426 7114.852 7140.778 7118.578 0.7844097 0.1866667 2 3 -3550.426 7122.852 7163.594 7128.708 0.7145465 0.1800000 3 4 -3550.428 7130.857 7186.414 7138.843 0.3259081 0.2000000 n_params converged 1 7 TRUE 2 11 TRUE 3 15 TRUE Convergence Diagnostics ======================= Number of random starts: 5 Best log-likelihood: -359.0618 Local maxima detected: 1 Top 5 solutions: rank loglik n_times diff_from_best 1 1 -359.0618 5 0 Warnings: - No convergence issues detected Recommendations: - Model appears well-identified Convergence Diagnostics ======================= Number of random starts: 5 Best log-likelihood: -359.0618 Local maxima detected: 1 Top 5 solutions: rank loglik n_times diff_from_best 1 1 -359.0618 5 0 Warnings: - No convergence issues detected Recommendations: - Model appears well-identified Saving _problems/test-growth-models-84.R Growth Mixture Model Selection ============================== Models compared: 1, 2 Criteria used: BIC Recommended classes: 1 Comparison Table: n_classes loglik aic bic abic entropy smallest_class 1 -363.5008 733.0015 738.7376 729.3211 NaN 1 2 -363.4939 740.9877 754.3719 732.4000 0.007483237 1 n_params converged 3 TRUE 7 TRUE --- Access fitted models: object@fitted_models BLRT results: object@blrt_results Growth Mixture Model Selection ============================== Models compared: 1, 2 Criteria used: BIC Recommended classes: 1 Comparison Table: n_classes loglik aic bic abic entropy smallest_class 1 -363.5008 733.0015 738.7376 729.3211 NaN 1 2 -363.4939 740.9877 754.3719 732.4000 0.007483237 1 n_params converged 3 TRUE 7 TRUE --- Access fitted models: object@fitted_models BLRT results: object@blrt_results Saving _problems/test-model-selection-401.R [ FAIL 2 | WARN 91 | SKIP 73 | PASS 744 ] ══ Skipped tests (73) ══════════════════════════════════════════════════════════ • Binary distal outcomes require special handling - implement in v0.3.0 (1): 'test-r3step.R:361:3' • Cross-sectional validation not yet implemented in gmm_survey() (1): 'test-edge-cases.R:379:3' • ML method not yet implemented (1): 'test-r3step.R:399:3' • ML method not yet implemented in r3step (1): 'test-r3step.R:49:3' • Mplus comparison requires Mplus installation - test manually (1): 'test-comprehensive.R:423:3' • Mplus conversion requires Mplus syntax parser - implement in future (1): 'test-utilities.R:118:3' • Mplus export requires template - implement in future (1): 'test-utilities.R:138:3' • On CRAN (51): 'test-convergence.R:156:3', 'test-convergence.R:186:3', 'test-convergence.R:220:3', 'test-convergence.R:260:3', 'test-convergence.R:304:3', 'test-convergence.R:337:3', 'test-convergence.R:376:3', 'test-convergence.R:407:3', 'test-convergence.R:440:3', 'test-convergence.R:481:3', 'test-convergence.R:515:3', 'test-convergence.R:542:3', 'test-convergence.R:571:3', 'test-convergence.R:599:3', 'test-edge-cases.R:5:3', 'test-edge-cases.R:34:3', 'test-edge-cases.R:61:3', 'test-edge-cases.R:94:3', 'test-edge-cases.R:129:3', 'test-edge-cases.R:160:3', 'test-edge-cases.R:191:3', 'test-edge-cases.R:221:3', 'test-edge-cases.R:262:3', 'test-edge-cases.R:290:3', 'test-edge-cases.R:347:3', 'test-edge-cases.R:428:3', 'test-edge-cases.R:459:3', 'test-edge-cases.R:492:3', 'test-edge-cases.R:528:3', 'test-model-selection.R:180:3', 'test-model-selection.R:224:3', 'test-model-selection.R:251:3', 'test-model-selection.R:283:3', 'test-model-selection.R:316:3', 'test-model-selection.R:347:3', 'test-model-selection.R:405:3', 'test-model-selection.R:435:3', 'test-model-selection.R:467:3', 'test-model-selection.R:496:3', 'test-model-selection.R:526:3', 'test-model-selection.R:565:3', 'test-plotting-edge-cases.R:5:3', 'test-plotting-edge-cases.R:55:3', 'test-plotting-edge-cases.R:89:3', 'test-plotting-edge-cases.R:118:3', 'test-plotting-edge-cases.R:144:3', 'test-plotting-edge-cases.R:170:3', 'test-plotting-edge-cases.R:205:3', 'test-plotting-edge-cases.R:240:3', 'test-plotting-edge-cases.R:270:3', 'test-plotting-edge-cases.R:304:3' • Requires fitted models (2): 'test-lmr-cv.R:43:3', 'test-lmr-cv.R:56:3' • Requires fitted models - placeholder test (1): 'test-lmr-cv.R:22:3' • SurveyMixrRE class not yet fully implemented - pending v0.3.0 (1): 'test-random-effects.R:91:3' • SurveyMixrTVC class not yet fully implemented - pending v0.3.0 (1): 'test-time-varying-covariates.R:63:3' • check_missing_patterns() not yet implemented (1): 'test-missing-data.R:322:5' • compare_classes requires covariates in @data - functionality needs review (2): 'test-comprehensive.R:357:3', 'test-comprehensive.R:392:3' • empty test (3): 'test-diagnostics-advanced.R:83:1', 'test-lmr-cv.R:273:1', 'test-missing-data.R:270:1' • gmm_survey_tvc not yet implemented - pending v0.3.0 (1): 'test-time-varying-covariates.R:15:3' • nonlinear growth model not yet implemented (1): 'test-growth-models.R:117:3' • plot_class_comparison requires covariates in @data - functionality needs review (1): 'test-comprehensive.R:513:3' • plotly is available (1): 'test-plotting-interactive.R:24:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-growth-models.R:84:3'): quadratic growth model works correctly ── Expected `any(grepl("quadratic", names(params)))` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE ── Failure ('test-model-selection.R:390:3'): gmm_select error handling for invalid classes parameter ── `gmm_select(...)` threw an error with unexpected message. Expected match: "classes must be in ascending order" Actual message: "undefined columns selected" Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-model-selection.R:390:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─surveymixr::gmm_select(...) 7. └─surveymixr:::compute_blrt(...) 8. └─surveymixr:::generate_data_from_fit(fit_k1, data, id, time, outcome) 9. ├─original_data[, c(id, time, outcome, names(fit@survey_design))] 10. └─base::`[.data.frame`(original_data, , c(id, time, outcome, names(fit@survey_design))) [ FAIL 2 | WARN 91 | SKIP 73 | PASS 744 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s] OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... [16s] OK * DONE Status: 1 ERROR, 2 NOTEs