* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ausoa.Rcheck’ * using R Under development (unstable) (2025-09-11 r88813) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘ausoa/DESCRIPTION’ ... OK * this is package ‘ausoa’ version ‘2.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Dylan Mordaunt ’ New submission Possibly misspelled words in DESCRIPTION: Microsimulation (2:10) microsimulation (6:38) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "AUS-OA", family = "Team", role = "aut", email = "dylan.mordaunt@vuw.ac.nz"), person(given = "Dylan", family = "Mordaunt", role = "cre", email = "dylan.mordaunt@vuw.ac.nz")) as necessary. Package has a VignetteBuilder field but no prebuilt vignette index. Size of tarball: 18526385 bytes * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'data.table', 'dplyr', 'forcats', 'ggplot2', 'here', 'magrittr', 'purrr', 'ragg', 'readr', 'rlang', 'scales', 'tidyr', 'yaml' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘ausoa’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: ‘CHEAT_SHEET.md’ ‘CRAN_READINESS.md’ ‘CRAN_SUBMISSION_GUIDE.md’ ‘DATASET_SOURCING_PLAN.md’ ‘DESCRIPTION.backup’ ‘Dockerfile.test’ ‘OA_REFOCUS_PLAN.md’ ‘ONBOARDING_CHECKLIST.md’ ‘R-CMD-check-enhanced.yaml’ ‘RELEASE_GUIDE_v2.0.1.md’ ‘REPOSITORY_ENHANCEMENT_SUMMARY.ps1’ ‘TEAM_TRAINING_GUIDE.md’ ‘TRAINING_PRESENTATION.md’ ‘WORKFLOW_OVERVIEW.md’ ‘_pkgdown.yml’ ‘build_docs.R’ ‘build_package.R’ ‘check_cran_readiness.R’ ‘check_desc.R’ ‘check_devtools.R’ ‘convert_files.R’ ‘cran-comments.md’ ‘cran_advanced_submit.R’ ‘cran_auto_submit.R’ ‘cran_check_results’ ‘cran_dashboard.R’ ‘cran_followup.R’ ‘cran_prep.R’ ‘cran_submit.R’ ‘cran_submit.bat’ ‘cran_summary.R’ ‘cran_workflow.R’ ‘final_ceac_test.R’ ‘install_missing_packages.R’ ‘install_simPop.R’ ‘install_styler.R’ ‘prepare_cran_submission.R’ ‘regen_namespace.R’ ‘release_notes.md’ ‘run_cran_prep.R’ ‘run_test.R’ ‘simple_build.R’ ‘simple_test.R’ ‘temp_build_docs.R’ ‘test_enhanced_ceac.R’ ‘test_enhanced_viz.R’ ‘test_packages.R’ ‘tutorials’ ‘validate_desc.R’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: Cannot extract version info from the following section titles: ausoa NEWS * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘arrow’ ‘caret’ ‘pdp’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s/11s] NOTE analyze_parameter_correlations : : no visible global function definition for ‘cor’ analyze_parameter_correlations: no visible global function definition for ‘lm’ analyze_parameter_correlations: no visible global function definition for ‘residuals’ analyze_parameter_correlations: no visible global function definition for ‘cor’ analyze_parameter_influence: no visible global function definition for ‘quantile’ analyze_treatment_effectiveness: no visible global function definition for ‘sd’ analyze_treatment_effectiveness: no visible global function definition for ‘median’ assess_calibration: no visible global function definition for ‘quantile’ assess_calibration: no visible global function definition for ‘pchisq’ assess_psa_convergence: no visible global function definition for ‘quantile’ assess_psa_convergence: no visible global function definition for ‘sd’ calculate_convergence_diagnostics: no visible global function definition for ‘sd’ calculate_convergence_diagnostics: no visible global function definition for ‘quantile’ calculate_costs_fcn: no visible binding for global variable ‘productivity_cost’ calculate_nmb: no visible global function definition for ‘sd’ calculate_nmb: no visible global function definition for ‘median’ calculate_nmb: no visible global function definition for ‘quantile’ calculate_prediction_uncertainty: no visible binding for global variable ‘var’ calculate_prediction_uncertainty: no visible binding for global variable ‘sd’ create_feature_pipeline: no visible global function definition for ‘median’ create_feature_pipeline: no visible binding for global variable ‘.’ create_feature_pipeline: no visible binding for global variable ‘comorbidities’ create_feature_pipeline: no visible binding for global variable ‘surgical_approach’ create_feature_pipeline: no visible binding for global variable ‘implant_type’ create_model_ensemble : : no visible global function definition for ‘predict’ create_psa_visualization_report: no visible global function definition for ‘plot_parameter_distributions’ create_risk_stratification: no visible global function definition for ‘quantile’ create_risk_stratification: no visible binding for global variable ‘median’ create_synthetic_abs_data : : no visible global function definition for ‘rpois’ create_synthetic_abs_data : : no visible global function definition for ‘rbeta’ create_synthetic_nhs_data: no visible global function definition for ‘rbinom’ create_synthetic_nhs_data: no visible global function definition for ‘plogis’ create_synthetic_nhs_data: no visible binding for global variable ‘osteoarthritis’ create_synthetic_nhs_data: no visible global function definition for ‘rbeta’ create_synthetic_nhs_data: no visible global function definition for ‘rpois’ create_synthetic_oai_data: no visible global function definition for ‘plogis’ create_synthetic_oai_data: no visible global function definition for ‘rbinom’ create_synthetic_oai_data: no visible global function definition for ‘rbeta’ extract_feature_importance: no visible global function definition for ‘methods’ generate_ceac_bootstrap: no visible binding for global variable ‘quantile’ generate_interpretability_report: no visible global function definition for ‘desc’ generate_interpretability_report: no visible binding for global variable ‘Overall’ generate_interpretability_report: no visible global function definition for ‘head’ generate_psa_report: no visible global function definition for ‘sd’ generate_psa_report: no visible global function definition for ‘median’ generate_psa_report: no visible global function definition for ‘quantile’ load_ml_packages: no visible global function definition for ‘installed.packages’ load_ml_packages: no visible global function definition for ‘install.packages’ plot_ceac: no visible binding for global variable ‘wtp’ plot_ceac: no visible binding for global variable ‘probability_ce’ plot_ceac_bootstrap: no visible binding for global variable ‘wtp’ plot_ceac_bootstrap: no visible binding for global variable ‘probability_ce’ plot_ceac_bootstrap: no visible binding for global variable ‘ci_lower’ plot_ceac_bootstrap: no visible binding for global variable ‘ci_upper’ plot_convergence_diagnostics: no visible binding for global variable ‘outcome’ plot_convergence_diagnostics: no visible binding for global variable ‘ci_width’ plot_convergence_diagnostics: no visible binding for global variable ‘ci_converged’ plot_convergence_diagnostics: no visible binding for global variable ‘relative_se’ plot_convergence_diagnostics: no visible binding for global variable ‘rse_converged’ plot_nmb_distribution: no visible binding for global variable ‘metric’ plot_nmb_distribution: no visible binding for global variable ‘value’ plot_nmb_distribution: no visible binding for global variable ‘type’ plot_parameter_correlations: no visible global function definition for ‘reorder’ plot_parameter_correlations: no visible binding for global variable ‘parameter’ plot_parameter_correlations: no visible binding for global variable ‘abs_correlation’ plot_parameter_correlations: no visible binding for global variable ‘pearson_correlation’ plot_psa_scatter: no visible binding for global variable ‘incremental_qaly’ plot_psa_scatter: no visible binding for global variable ‘incremental_cost’ plot_psa_scatter: no visible binding for global variable ‘cost_effective’ plot_psa_scatter: no visible binding for global variable ‘qaly’ plot_psa_scatter: no visible binding for global variable ‘cost’ plot_sensitivity_analysis: no visible global function definition for ‘complete.cases’ plot_sensitivity_analysis: no visible global function definition for ‘reorder’ plot_sensitivity_analysis: no visible binding for global variable ‘parameter’ plot_sensitivity_analysis: no visible binding for global variable ‘elasticity’ plot_tornado_diagram: no visible binding for global variable ‘base’ plot_tornado_diagram: no visible binding for global variable ‘value’ plot_tornado_diagram: no visible global function definition for ‘reorder’ plot_tornado_diagram: no visible binding for global variable ‘parameter’ plot_tornado_diagram: no visible binding for global variable ‘influence’ plot_tornado_diagram: no visible binding for global variable ‘type’ plot_voi_analysis: no visible binding for global variable ‘value’ plot_voi_analysis: no visible binding for global variable ‘type’ predict_complication_risk: no visible global function definition for ‘rbinom’ predict_complication_risk: no visible global function definition for ‘predict’ predict_progression: no visible global function definition for ‘rbinom’ predict_treatment_response: no visible global function definition for ‘predict’ prepare_advanced_tutorial: no visible binding for global variable ‘.’ prepare_basic_tutorial: no visible binding for global variable ‘osteoarthritis’ run_psa_analysis : simulation_wrapper: no visible global function definition for ‘rbinom’ sample_parameters: no visible global function definition for ‘rbeta’ sample_parameters: no visible global function definition for ‘rgamma’ simulation_cycle_fcn: no visible binding for global variable ‘bmi_cat’ validate_ml_performance : : no visible global function definition for ‘predict’ validate_ml_performance: no visible global function definition for ‘predict’ validate_ml_performance: no visible global function definition for ‘cor’ Undefined global functions or variables: . Overall abs_correlation base bmi_cat ci_converged ci_lower ci_upper ci_width comorbidities complete.cases cor cost cost_effective desc elasticity head implant_type incremental_cost incremental_qaly influence install.packages installed.packages lm median methods metric osteoarthritis outcome parameter pchisq pearson_correlation plogis plot_parameter_distributions predict probability_ce productivity_cost qaly quantile rbeta rbinom relative_se reorder residuals rgamma rpois rse_converged sd surgical_approach type value var wtp Consider adding importFrom("stats", "complete.cases", "cor", "influence", "lm", "median", "pchisq", "plogis", "predict", "quantile", "rbeta", "rbinom", "reorder", "residuals", "rgamma", "rpois", "sd", "var") importFrom("utils", "head", "install.packages", "installed.packages", "methods") to your NAMESPACE file. * checking Rd files ... [0s/0s] 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 files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘ausoa-vignette.Rmd’ * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... WARNING '::' or ':::' imports not declared from: ‘bench’ ‘profmem’ ‘profvis’ 'library' or 'require' calls not declared from: ‘bench’ ‘caret’ ‘hedgehog’ ‘pROC’ ‘profvis’ * checking tests ... [5s/5s] OK Running ‘test_ml_framework.R’ [1s/1s] Running ‘test_ml_integration.R’ [1s/1s] Running ‘test_predictive_modeling.R’ [1s/1s] Running ‘test_psa_framework.R’ [1s/1s] Running ‘testthat.R’ [2s/2s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... WARNING Directory 'inst/doc' does not exist. Package vignette without corresponding single PDF/HTML: ‘ausoa-vignette.Rmd’ * checking re-building of vignette outputs ... [2s/2s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 4 NOTEs