* 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)