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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(PregnancyIdentifier) > > test_check("PregnancyIdentifier") Starting 2 test processes. > test-compareWithPET-pregnancyExtension.R: trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/empty_cdm_5.4.zip' > test-attrition.R: trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/empty_cdm_5.4.zip' > test-compareWithPET-pregnancyExtension.R: Content type 'application/zip' length 772029174 bytes (736.3 MB) > test-attrition.R: Content type 'application/zip' length 772029174 bytes (736.3 MB) > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-compareWithPET-pregnancyExtension.R: = > test-attrition.R: = > test-attrition.R: = > test-attrition.R: downloaded 736.3 MB > test-attrition.R: > test-attrition.R: > test-attrition.R: Download completed! > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: = > test-compareWithPET-pregnancyExtension.R: downloaded 736.3 MB > test-compareWithPET-pregnancyExtension.R: > test-compareWithPET-pregnancyExtension.R: > test-compareWithPET-pregnancyExtension.R: Download completed! > test-compareWithPET-pregnancyExtension.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-compareWithPET-pregnancyExtension.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-compareWithPET-pregnancyExtension.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-compareWithPET-pregnancyExtension.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-compareWithPET-pregnancyExtension.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-compareWithPET-pregnancyExtension.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-compareWithPET-pregnancyExtension.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_compareWithPET_extension_out/export > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-compareWithPET-pregnancyExtension.R: Reading file: 'D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_compareWithPET_extension_export/pet_comparison_summarised_result.csv'. > test-compareWithPET-pregnancyExtension.R: Converting to summarised_result: 'D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_compareWithPET_extension_export/pet_comparison_summarised_result.csv'. > test-attrition.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-attrition.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-attrition.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_attrition_pipeline/export > test-compareWithPET.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-compareWithPET.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-compareWithPET.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-compareWithPET.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-compareWithPET.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-compareWithPET.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-compareWithPET.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_compareWithPET_out/export > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-compareWithPET.R: Reading file: 'D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_compareWithPET_export/pet_comparison_summarised_result.csv'. > test-compareWithPET.R: Converting to summarised_result: 'D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_compareWithPET_export/pet_comparison_summarised_result.csv'. > test-attrition.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-attrition.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-attrition.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_attrition_consistency/export Saving _problems/test-db-spark-7.R > test-deliveryMode.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-deliveryMode.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-deliveryMode.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-deliveryMode.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-deliveryMode.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-deliveryMode.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-deliveryMode.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/testHipps/export > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-attrition.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-attrition.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-attrition.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_attrition_export_out/export > test-attrition.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-attrition.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-attrition.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_attrition_export_dir > test-exportPregnancies.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-exportPregnancies.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-exportPregnancies.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-exportPregnancies.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-exportPregnancies.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_exportPregnancies/export > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-exportPregnancies.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_exportPregnancies_export > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-attrition.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-attrition.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-attrition.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-attrition.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-attrition.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_attrition_by_outcome/export > test-exportPregnancies.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-exportPregnancies.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-exportPregnancies.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-exportPregnancies.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-exportPregnancies.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_exportPregnancies_custom/export > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-exportPregnancies.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-exportPregnancies.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\Rtmpc37T7t/test_exportPregnancies_export_custom > test-initPregnancies.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-initPregnancies.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-initPregnancies.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-initPregnancies.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-initPregnancies.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-initPregnancies.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-initPregnancies.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_preg_final/export > test-outcome_category.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-outcome_category.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-outcome_category.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-outcome_category.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-outcome_category.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-outcome_category.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-outcome_category.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_outcome_category/export > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-outcome_category.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-outcome_category.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-outcome_category.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-outcome_category.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-outcome_category.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-outcome_category.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-outcome_category.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_ga_lb_35_38/export > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runEsd.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runEsd.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runPregnancyIdentifier.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runPregnancyIdentifier.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runPregnancyIdentifier.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runPregnancyIdentifier.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runPregnancyIdentifier.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-runPregnancyIdentifier.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-runPregnancyIdentifier.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_runPregnancyIdentifier/export > test-runPregnancyIdentifier.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runPregnancyIdentifier.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runPregnancyIdentifier.R: ! 6 concept(s) from domain NA eliminated as it is not supported. > test-runPregnancyIdentifier.R: i Supported domains are: device, specimen, measurement, drug, condition, observation, procedure, episode, and visit. > test-runPregnancyIdentifier.R: fix_start_before_end: episodes with start >= end before fix: 0 > test-runPregnancyIdentifier.R: fix_start_before_end: episodes with start >= end after fix: 0 > test-runPregnancyIdentifier.R: Files have been written to: D:\temp\2026_03_07_07_45_17_16671\RtmpeWXiTO/test_runPregnancyIdentifier_custom/export [ FAIL 1 | WARN 0 | SKIP 4 | PASS 259 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-shiny-app.R:9:3' • Sys.getenv("CDM5_POSTGRESQL_DBNAME") == "" is TRUE (1): 'test-db-postgres.R:7:3' • Sys.getenv("CDM5_SQL_SERVER_CDM_DATABASE") == "" is TRUE (1): 'test-db-sqlserver.R:5:3' • Sys.getenv("SNOWFLAKE_SERVER") == "" is TRUE (1): 'test-db-snowflake.R:8:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-db-spark.R:7:3'): runPregnancyIdentifier on SPARK/Databricks ─── Error in `get_connection("spark")`: Could not create connection. Are some environment variables missing? Backtrace: ▆ 1. └─PregnancyIdentifier:::get_connection("spark") at test-db-spark.R:7:3 2. └─rlang::abort("Could not create connection. Are some environment variables missing?") at ./helper-db.R:84:3 [ FAIL 1 | WARN 0 | SKIP 4 | PASS 259 ] Error: ! Test failures. Execution halted