R Under development (unstable) (2025-03-09 r87914 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(CdmOnboarding) > > test_check("CdmOnboarding") Downloading synpuf-1k trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Download completed! Creating CDM database D:\temp\2025_03_10_17_40_17_3168\RtmpemhuIK\file2b988140f79d9/synpuf-1k_5.3.zip ■■■■■■■■■■■■■■■■■■■■ 63% | ETA: 1s ■■■■■■■■■■■■■■■■■■■■■■■■■ 80% | ETA: 1s Generated: Visits to the Intensive Care Unit Generated: Type 2 Diabetes Generated: Guillain Barré syndrome Generated: Kawasaki Generated: Myocarditis Generated: Haemorrhagic stroke Generated: Ischaemic stroke Generated: COVID-19 Connecting using DuckDB driver > 'data_tables_count.sql' executed successfully in 0.12 secs Connecting using DuckDB driver > 'totalrecords.sql' executed successfully in 0.07 secs Connecting using DuckDB driver > 'recordsperperson.sql' executed successfully in 0.08 secs Connecting using DuckDB driver > 'conceptsperperson.sql' executed successfully in 0.07 secs Connecting using DuckDB driver > 'observation_period_length.sql' executed successfully in 0.08 secs Connecting using DuckDB driver > 'active_persons.sql' executed successfully in 0.07 secs Connecting using DuckDB driver > 'observed_by_month.sql' executed successfully in 0.06 secs Connecting using DuckDB driver > 'date_range_by_type_concept.sql' executed successfully in 0.18 secs Connecting using DuckDB driver > 'day_of_the_week.sql' executed successfully in 0.16 secs Connecting using DuckDB driver > 'day_of_the_month.sql' executed successfully in 0.12 secs Connecting using DuckDB driver > 'observation_periods_per_person.sql' executed successfully in 0.06 secs Connecting using DuckDB driver > 'observation_period_overlap.sql' executed successfully in 0.06 secs Connecting using DuckDB driver > 'day_month_year_of_birth.sql' executed successfully in 0.11 secs Connecting using DuckDB driver > 'visit_length.sql' executed successfully in 0.19 secs Starting execution of DrugExposureDiagnostics for 11 ingredients i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:42:13.798568 v Summary finished, at 2025-03-10 17:42:14.742589 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:42:22.703785 v Summary finished, at 2025-03-10 17:42:23.300516 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:42:31.441266 v Summary finished, at 2025-03-10 17:42:32.016916 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:42:40.144959 v Summary finished, at 2025-03-10 17:42:41.024396 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:42:49.686523 v Summary finished, at 2025-03-10 17:42:50.314697 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:43:05.219708 v Summary finished, at 2025-03-10 17:43:06.019796 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:43:14.001245 v Summary finished, at 2025-03-10 17:43:14.567395 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:43:22.82054 v Summary finished, at 2025-03-10 17:43:23.639845 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:43:32.313773 v Summary finished, at 2025-03-10 17:43:32.87523 i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2025-03-10 17:43:41.414878 v Summary finished, at 2025-03-10 17:43:41.965603 Executing DrugExposureDiagnostics took 103.66 seconds. Currently in a tryCatch or withCallingHandlers block, so unable to add global calling handlers. ParallelLogger will not capture R messages, errors, and warnings, only explicit calls to ParallelLogger. (This message will not be shown again this R session) Running CdmOnboarding v3.3.4 Running CdmOnboarding v3.3.4 Connecting using DuckDB driver > CDM Source table successfully extracted > CDM Source table successfully extracted Found database 'Synpuf' with CDM release date '2018-03-15' Found database 'Synpuf' with CDM release date '2018-03-15' Connecting using DuckDB driver Connecting using DuckDB driver > Achilles metadata successfully extracted > Achilles metadata successfully extracted Connecting using DuckDB driver Reading DataQualityDashboard results Reading DataQualityDashboard results > Successfully extracted DQD results overview from 'dqd_synpuf-1k.json' > Successfully extracted DQD results overview from 'dqd_synpuf-1k.json' > CDM Onboarding of database Synpuf started (cdm_version=v5.3) > CDM Onboarding of database Synpuf started (cdm_version=v5.3) > Done. > Done. > Complete CdmOnboarding took 0.01 minutes > Complete CdmOnboarding took 0.01 minutes > The CDM Onboarding results have been exported to . > The CDM Onboarding results have been exported to . > Saving doc to ./CdmOnboarding_synpuf-1k_20250310.docx > Saving doc to ./CdmOnboarding_synpuf-1k_20250310.docx > All generated CDM Onboarding results are bundled for sharing at: ./Results_Onboarding_synpuf-1k_20250310.zip > All generated CDM Onboarding results are bundled for sharing at: ./Results_Onboarding_synpuf-1k_20250310.zip Running CdmOnboarding v3.3.4 Connecting using DuckDB driver > CDM Source table successfully extracted Found database 'Synpuf' with CDM release date '2018-03-15' Connecting using DuckDB driver Connecting using DuckDB driver > Achilles metadata successfully extracted Connecting using DuckDB driver Warning: No dqdJsonPath specfied, data quality section will be empty. > CDM Onboarding of database Synpuf started (cdm_version=v5.3) > Done. > Complete CdmOnboarding took 0.01 minutes > The CDM Onboarding results have been exported to . > Saving doc to ./CdmOnboarding_synpuf-1k_20250310.docx > All generated CDM Onboarding results are bundled for sharing at: ./Results_Onboarding_synpuf-1k_20250310.zip Connecting using DuckDB driver > Retrieving duration of Achilles queries in 0.07 secs Connecting using DuckDB driver > Executing vocabulary query benchmark in 0.60 secs Starting execution of CDMConnector Benchmark Getting distinct count of concept relationship table Getting count of different relationship IDs in concept relationship table Getting join of concept and concept class computed to a temp table Getting concept table collected into memory Getting join of person and observation period collected into memory Getting summary of observation period start and end dates by gender concept id Warning: The applied indexes query cannot be run for 'duckdb', it is only implemented for PostgreSQL and MS Sql Server. Loading required package: benchmarkme Running Performance Checks on AMD EPYC 7443 24-Core Processor cpu with 96 cores, and 274.73 GB ram. Connecting using DuckDB driver > DBMS version found: "v1.2.0" Connecting using DuckDB driver > Count on vocabulary tables query executed successfully in 0.06 secs Connecting using DuckDB driver > Concept counts by vocabulary query executed successfully in 0.18 secs Connecting using DuckDB driver > Source to concept map breakdown query executed successfully in 0.06 secs Connecting using DuckDB driver > Source to concept map query executed successfully in 0.06 secs Connecting using DuckDB driver Starting vocab mapping queries. Preprocessing domains... > Mapping Temp tables query executed successfully in 0.16 secs > Mapping Completeness query executed successfully in 0.02 secs > Drug Level Mapping query executed successfully in 0.06 secs > Unmapped drugs query executed successfully in 0.01 secs > Unmapped conditions query executed successfully in 0.01 secs > Unmapped measurements query executed successfully in 0.01 secs > Unmapped observations query executed successfully in 0.00 secs > Unmapped procedures query executed successfully in 0.00 secs > Unmapped devices query executed successfully in 0.00 secs > Unmapped visits query executed successfully in 0.00 secs > Unmapped visit details query executed successfully in 0.00 secs > Unmapped meas units query executed successfully in 0.01 secs > Unmapped obs units query executed successfully in 0.01 secs > Unmapped meas values query executed successfully in 0.01 secs > Unmapped obs values query executed successfully in 0.01 secs > Unmapped drug route query executed successfully in 0.01 secs > Unmapped specialty query executed successfully in 0.00 secs > Mapped drugs query executed successfully in 0.09 secs > Mapped conditions query executed successfully in 0.12 secs > Mapped measurements query executed successfully in 0.05 secs > Mapped observations query executed successfully in 0.07 secs > Mapped procedures query executed successfully in 0.04 secs > Mapped devices query executed successfully in 0.02 secs > Mapped visits query executed successfully in 0.02 secs > Mapped visit details query executed successfully in 0.01 secs > Mapped meas units query executed successfully in 0.02 secs > Mapped obs units query executed successfully in 0.02 secs > Mapped meas values query executed successfully in 0.02 secs > Mapped obs values query executed successfully in 0.02 secs > Mapped drug routes query executed successfully in 0.01 secs > Mapped specialty query executed successfully in 0.01 secs [ FAIL 0 | WARN 22 | SKIP 4 | PASS 68 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • covered by individual tests (1): 'test-full.R:2:3' • not used (2): 'test-dataTablesChecksOptimize.R:2:3', 'test-vocabularyChecksOptimize.R:2:3' • requires network connection (1): 'test-webapiChecks.R:2:3' [ FAIL 0 | WARN 22 | SKIP 4 | PASS 68 ] > > proc.time() user system elapsed 375.90 82.21 174.46