* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘UKBAnalytica’ ... ** this is package ‘UKBAnalytica’ version ‘1.0.0’ ** package ‘UKBAnalytica’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘UKBAnalytica’ finding HTML links ... done UKBAnalytica html aggregate_cancer_registry_earliest html aggregate_death_as_diagnosis html aggregate_icd10_earliest html aggregate_icd9_earliest html aggregate_opcs4_earliest html aggregate_self_report_earliest html assess_balance html build_full_cohort html build_survival_dataset html calculate_air_pollution html calculate_blood_pressure html calculate_diet_score html calculate_weights html classify_metabolites html coef.mediation_result html combine_disease_definitions html compare_data_sources html compute_protein_ppi_metrics html confint.mediation_result html create_baseline_table html create_disease_definition html create_imputation_list html create_medication_definition html dot-calculate_baseline html dot-check_ml_package html dot-create_shap_predict_wrapper html dot-fit_coxnet html dot-fit_gbm_surv html dot-fit_glmnet html dot-fit_logistic html dot-fit_nnet html dot-fit_rf html dot-fit_rsf html dot-fit_svm html dot-fit_xgboost html dot-get_model_label html dot-get_processor html dot-get_variable_mapping html dot-parse_formula html dot-prepare_model_data html dot-split_data html estimate_propensity_score html extract_cases_by_source html extract_diabetes_subtype_baseline html extract_disease_diagnosis html extract_disease_history html extract_disease_history_sensitivity html extract_medications html extract_self_report_medications html filter_cancer_registry html filter_death_codes html filter_icd10_codes html filter_icd9_codes html filter_opcs4_codes html filter_self_report_codes html fit_mi_models html generate_wide_format_dual_source html get_death_dates html get_disease_catalog html get_field_info html get_field_metadata html get_medication_catalog html get_pomegranate_diseases html get_pomegranate_source_manifest html get_predefined_diseases html get_predefined_medications html get_protein_ppi html get_ukb_demo_colnames html get_variable_info html get_variable_set html get_variable_sets html load_pomegranate_portal_coding html load_ukb_medication_coding html load_ukb_metabolite_panel html match_propensity html metabolite_to_metaboanalyst_name html mi_pool html ml_evaluate html ml_model html ml_shap html ml_survival html parse_cancer_registry html parse_death_records html parse_icd10_diagnoses html parse_icd9_diagnoses html parse_opcs4_procedures html parse_self_reported_illnesses html plot.ukb_ml_flow html plot.ukb_ml_flow_compare html plot_balance html plot_calibration html plot_correlation html plot_cox_loghr_correlation html plot_cox_sensitivity_correlation html plot_enrichment_lollipop html plot_forest html plot_go_ora_bar html plot_heatmap html plot_km_curve html plot_mediation html plot_mediation_forest html plot_metabolite_ora_barplot html plot_metabolite_ora_dotplot html plot_mi_diagnostics html plot_mi_pooled html plot_ml_calibration html plot_ml_compare html plot_ml_confusion html plot_ml_dca html plot_ml_gain html plot_ml_importance html plot_ml_ks html plot_ml_lift html plot_ml_pr html plot_ml_roc html plot_ml_roc_compare html plot_participant_flow html plot_ps_distribution html plot_rcs html plot_regression_volcano html plot_scatter html plot_shap_beeswarm html plot_shap_dependence html plot_shap_force html plot_shap_summary html plot_stacked_bar html plot_top_hr_bars html plot_violin html pool_custom_estimates html pool_mi_models html preprocess_baseline html print.mediation_result html protein_to_gene_symbol html rank_protein_ppi_nodes html rap_extract html rap_extract_pheno html rap_find_dataset html rap_list_fields html rap_plan_extract html rap_submit_extract html regression_extensions html run_correlation html run_imputation html run_mediation html run_metabolite_ora html run_multi_mediator html run_multi_subgroup html run_protein_kegg_ora html run_protein_ora html run_protein_ppi_clustering html run_protein_ppi_robustness html run_rcs html run_regression html run_sensitivity_mediation html run_subgroup_analysis html run_weighted_analysis html runmulti_competing html runmulti_cox html runmulti_cox_lag html runmulti_cox_zph html runmulti_gam html runmulti_glm html runmulti_lm html runmulti_logit html runmulti_negbin html runmulti_trend html score_protein_ppi_clusters html select_incident_by_years html sensitivity_exclude_early_events html sensitivity_exclude_missing_covariates html subset_protein_ppi html summary.mediation_result html tidy.mi_pooled_result html ukb_check_rap_env html ukb_clean_missing html ukb_compare_cox_results html ukb_compare_sensitivity_cox html ukb_cox_diagnostics html ukb_create_extraction_manifest html ukb_decode html ukb_decode_column_names html ukb_decode_values html ukb_demo html ukb_dictionary_zh html ukb_download_rap_dictionary html ukb_extract_fields html ukb_field_info html ukb_metadata_setup html ukb_ml_as_split html ukb_ml_calibration html ukb_ml_compare html ukb_ml_compare_feature_sets html ukb_ml_compare_flows html ukb_ml_confusion html ukb_ml_cv html ukb_ml_dca html ukb_ml_evaluate_test html ukb_ml_feature_select html ukb_ml_fit_final html ukb_ml_flow html ukb_ml_gain_lift html ukb_ml_importance html ukb_ml_ks html ukb_ml_metrics html ukb_ml_model html ukb_ml_pr html ukb_ml_predict html ukb_ml_roc html ukb_ml_roc_data html ukb_ml_split_data html ukb_ml_supported_models html ukb_ml_survival html ukb_ml_survival_as_split html ukb_ml_survival_evaluate_test html ukb_ml_survival_feature_select html ukb_ml_survival_fit_final html ukb_ml_survival_importance html ukb_ml_survival_predict html ukb_ml_survival_shap html ukb_ml_survival_split_data html ukb_ml_survival_tune html ukb_ml_survival_workflow html ukb_ml_threshold html ukb_ml_tune html ukb_ml_workflow html ukb_participant_flow html ukb_protein_annotation html ukb_query_dictionary html ukb_scale_with_parameters html ukb_search_fields html ukb_sensitivity_suite html ukb_shap html ukb_shap_dependence html ukb_shap_force html ukb_shap_summary html ukb_snapshot html ukb_standardize_by_train html ukb_time_skeleton html ukb_top_hr_results html ukb_train_validation_cox html ukb_validate_columns html ukb_write_extraction_manifest html variable_preprocess html *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (UKBAnalytica)