├── .Rbuildignore ├── .devcontainer.json ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── package_test.yaml │ ├── pkgdown.yaml │ ├── test-covbadge.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── assess_pkg.R ├── assess_pkg_r_package.R ├── badges.R ├── capture_cran_warning.R ├── check_suggested_exp_funcs.R ├── contains_R_folder.R ├── contains_vignette_folder.R ├── core_metrics.R ├── create_empty_results.R ├── create_empty_tm.R ├── create_traceability_matrix.R ├── dependencies.R ├── dependency_tree.R ├── documentation_metrics.R ├── extract_thresholds.R ├── generate_html_report.R ├── generate_traceability_matrix.R ├── get_bioconductor_data.R ├── get_download.R ├── get_exports.R ├── get_func_descriptions.R ├── get_github_data.R ├── get_package_host_info.R ├── get_pubmed_data.R ├── get_risk_analysis.R ├── get_session_dependencies.R ├── get_suggested_exp_funcs.R ├── globals.R ├── install_package_local.R ├── modify_description_file.R ├── risk_assess_pkg.R ├── risk_assess_pkg_lock_files.R ├── sanofi.risk.assessr-package.R ├── set_up_pkg.R ├── setup_rcmdcheck_args.R ├── unittest_methods.R ├── unpack_tarball.R └── utils.R ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── inst ├── config │ └── risk-definition.json ├── examples │ ├── assessr.R │ └── risk_report_ggplot2_3.5.2.html ├── report_templates │ └── risk_report_template.Rmd └── test-data │ ├── check_vignettes │ ├── got_vignette.tar.gz │ ├── got_vignette.teeeeeeear │ ├── just_vignette_folder.tar.gz │ └── no_vignette.tar.gz │ ├── diffdf-1.0.4.tar.gz │ ├── empty.tar.gz │ ├── here-1.0.1.tar.gz │ ├── package_test_case.csv │ ├── riskdata_results_slim.csv │ ├── stringr-1.5.1.tar.gz │ ├── test.package.0001_0.1.0.tar.gz │ ├── test.package.0002_0.1.0.tar.gz │ ├── test.package.0003_0.1.0.tar.gz │ ├── test.package.0004_0.1.0.tar.gz │ ├── test.package.0005_0.1.0.tar.gz │ ├── test.package.0006_0.1.0.tar.gz │ ├── test.package.0007_0.1.0.tar.gz │ ├── test.package.0008_0.1.0.tar.gz │ ├── test.package.0009_0.1.0.tar.gz │ ├── test.package.0010_0.1.0.tar.gz │ ├── test.package.0011_0.1.0.tar.gz │ ├── test.package.0012_0.1.0.tar.gz │ └── test.package.0013_0.1.0.tar.gz ├── man ├── as_iso_date.Rd ├── assess_description_file_elements.Rd ├── assess_examples.Rd ├── assess_export_help.Rd ├── assess_exports.Rd ├── assess_news.Rd ├── assess_news_current.Rd ├── assess_pkg.Rd ├── assess_pkg_r_package.Rd ├── assess_size_codebase.Rd ├── assess_vignettes.Rd ├── average_issue_close_time.Rd ├── bioconductor_reverse_deps.Rd ├── build_dependency_tree.Rd ├── capture_cran_warning.Rd ├── check_and_fetch_cran_package.Rd ├── check_cran_package.Rd ├── check_forbidden_notes.Rd ├── check_ggproto.Rd ├── check_pkg_tests_and_snaps.Rd ├── check_suggested_exp_funcs.Rd ├── classify_function_body.Rd ├── clean_license.Rd ├── clean_up_dependencies.Rd ├── compute_risk.Rd ├── contains_r_folder.Rd ├── contains_vignette_folder.Rd ├── convert_number_to_abbreviation.Rd ├── convert_number_to_percent.Rd ├── count_commits_last_months.Rd ├── cran_packages.Rd ├── cran_revdep.Rd ├── create_empty_results.Rd ├── create_empty_tm.Rd ├── create_file_coverage_df.Rd ├── create_items_matched.Rd ├── create_traceability_matrix.Rd ├── dependsOnPkgs.Rd ├── detect_version_conflicts.Rd ├── doc_riskmetric.Rd ├── download_and_parse_dependencies.Rd ├── expand_dependency_type_spec.Rd ├── extract_dependency_package_names.Rd ├── extract_exported_function_info.Rd ├── extract_ggproto_methods.Rd ├── extract_maintainer_info.Rd ├── extract_package_name.Rd ├── extract_package_version.Rd ├── extract_risk_inputs.Rd ├── extract_thresholds_by_id.Rd ├── extract_thresholds_by_key.Rd ├── extract_version.Rd ├── fetch_all_dependencies.Rd ├── fetch_bioconductor_package_info.Rd ├── fetch_bioconductor_releases.Rd ├── figures │ └── logo.png ├── filter_symbol_functions.Rd ├── find_reverse_dependencies.Rd ├── fine_grained_tms.Rd ├── function_is_ggproto.Rd ├── generate_coverage_section.Rd ├── generate_deps_section.Rd ├── generate_doc_metrics_section.Rd ├── generate_fg_trace_matrix_section.Rd ├── generate_html_report.Rd ├── generate_pop_metrics_section.Rd ├── generate_rcmd_check_section.Rd ├── generate_rev_deps_section.Rd ├── generate_risk_details.Rd ├── generate_risk_summary.Rd ├── generate_trace_matrix_section.Rd ├── generate_traceability_matrix.Rd ├── get_all_s4_methods.Rd ├── get_bioconductor_package_url.Rd ├── get_commits_since.Rd ├── get_cran_package_url.Rd ├── get_cran_total_downloads.Rd ├── get_dependencies.Rd ├── get_exports.Rd ├── get_func_descriptions.Rd ├── get_github_data.Rd ├── get_host_package.Rd ├── get_internal_package_url.Rd ├── get_license_thresholds.Rd ├── get_max_thresholds.Rd ├── get_package_download_bioconductor.Rd ├── get_package_download_cran.Rd ├── get_pkg_author.Rd ├── get_pkg_desc.Rd ├── get_pkg_license.Rd ├── get_pkg_name.Rd ├── get_pubmed_by_year.Rd ├── get_pubmed_count.Rd ├── get_r6_methods_details.Rd ├── get_repo_owner.Rd ├── get_result_path.Rd ├── get_reverse_dependencies.Rd ├── get_risk_analysis.Rd ├── get_risk_definition.Rd ├── get_risk_metadata.Rd ├── get_s3_method.Rd ├── get_session_dependencies.Rd ├── get_suggested_exp_funcs.Rd ├── get_toplevel_assignments.Rd ├── get_versions.Rd ├── handle_null.Rd ├── install_package_local.Rd ├── is_base.Rd ├── list_badges.Rd ├── map_functions_to_docs.Rd ├── map_functions_to_scripts.Rd ├── modify_description_file.Rd ├── normalize_data.Rd ├── parse_bioconductor_releases.Rd ├── parse_dcf_dependencies.Rd ├── parse_dcf_dependencies_version.Rd ├── parse_html_version.Rd ├── parse_package_info.Rd ├── preprocess_func_full_name.Rd ├── print_tree.Rd ├── process_items_matched.Rd ├── remove_base_packages.Rd ├── risk.assessr-package.Rd ├── risk_assess_pkg.Rd ├── risk_assess_pkg_lock_files.Rd ├── run_coverage.Rd ├── run_covr.Rd ├── run_rcmdcheck.Rd ├── safe_value.Rd ├── set_up_pkg.Rd ├── setup_rcmdcheck_args.Rd └── unpack_tarball.Rd ├── risk.assessr.Rproj ├── tests ├── testthat.R └── testthat │ ├── _snaps │ └── dependency_tree.md │ ├── setup.R │ ├── test-assess_pkg.R │ ├── test-assess_pkg_r_package.R │ ├── test-badges.R │ ├── test-bioconductor_reverse_deps.R │ ├── test-capture_cran_warning.R │ ├── test-check_forbidden_notes.R │ ├── test-check_suggested_exp_funcs.R │ ├── test-clean_up_dependencies.R │ ├── test-contains_r_folder.R │ ├── test-contains_vignette_folder.R │ ├── test-cran_packages.R │ ├── test-cran_revdep.R │ ├── test-create_empty_results.R │ ├── test-create_empty_tm.R │ ├── test-create_traceability_matrix.R │ ├── test-dependency_tree.R │ ├── test-dependsOnPkgs.R │ ├── test-documentation_metrics.R │ ├── test-expand_dependency_type_spec.R │ ├── test-extract_dependency_package_names.R │ ├── test-extract_thresholds.R │ ├── test-generate_html_report.R │ ├── test-generate_traceability_matrix.R │ ├── test-get_bioconductor_data.R │ ├── test-get_download.R │ ├── test-get_exports.R │ ├── test-get_github_data.R │ ├── test-get_package_host_info.R │ ├── test-get_pkg_name.R │ ├── test-get_pubmed_data.R │ ├── test-get_risk_analysis.R │ ├── test-get_session_dependencies.R │ ├── test-get_suggested_exp_funcs.R │ ├── test-get_toplevel_assignments.R │ ├── test-install_package_local.R │ ├── test-map_functions_to_scripts.R │ ├── test-modify_description_file.R │ ├── test-parse_dcf_dependencies.R │ ├── test-reverse_dependencies.R │ ├── test-risk_assess_pkg.R │ ├── test-risk_assess_pkg_lock_files.R │ ├── test-run_coverage.R │ ├── test-run_covr.R │ ├── test-run_rcmdcheck.R │ ├── test-set_up_pkg.R │ ├── test-setup_rcmdcheck_args.R │ ├── test-unittest_methods.R │ ├── test-unpack_tarball.R │ └── test-utils.R ├── vignettes ├── .gitignore ├── How-to-use-risk.assessr.Rmd ├── Popularity_metric.Rmd ├── Pubmed_data.Rmd ├── Traceability_matrix.Rmd ├── assets │ └── Picture1.png ├── define_custom_risk_rules.Rmd ├── dependency_tree.Rmd ├── examples.Rmd ├── generate_html_report.Rmd ├── get-available-version.Rmd ├── get-package-host.Rmd └── 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