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Type 'q()' to quit R. > library(testthat) > library(CohortGenerator) Loading required package: DatabaseConnector Loading required package: R6 > > test_check("CohortGenerator") attempting to download GiBleed trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB attempting to extract and load: D:\temp\RtmpWQBkQU/GiBleed_5.3.zip to: D:\temp\RtmpWQBkQU/GiBleed_5.3.sqlite Initiating cluster consisting only of main thread Generating cohort set took 1.05 secs Initiating cluster consisting only of main thread Generating cohort set took 0.99 secs Initiating cluster consisting only of main thread Generating cohort set took 0.18 secs Initiating cluster consisting only of main thread Generating cohort set took 0.49 secs Initiating cluster consisting only of main thread Generating cohort set took 0.72 secs Initiating cluster consisting only of main thread Generating cohort set took 0.17 secs Initiating cluster consisting only of main thread An error occurred while generating cohortName = Fail Cohort. Error: Error in `.createErrorReport()`: ! Error executing SQL: no such table: main.non_existant_table An error report has been created at d:/RCompile/CRANincoming/R-devel/CohortGenerator.Rcheck/tests/testthat/errorReportSql.txt [1] "Create cohorts with stopOnError = FALSE" Initiating cluster consisting only of main thread An error occurred while generating cohortName = Fail Cohort. Error: Error in `.createErrorReport()`: ! Error executing SQL: no such table: main.non_existant_table An error report has been created at d:/RCompile/CRANincoming/R-devel/CohortGenerator.Rcheck/tests/testthat/errorReportSql.txt Generating cohort set took 0.56 secs Initiating cluster consisting only of main thread An error occurred while generating cohortName = Fail Cohort. Error: Error in `.createErrorReport()`: ! Error executing SQL: no such table: main.non_existant_table An error report has been created at d:/RCompile/CRANincoming/R-devel/CohortGenerator.Rcheck/tests/testthat/errorReportSql.txt Generating cohort set took 0.87 secs Initiating cluster consisting only of main thread Generating cohort set took 0.31 secs trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB Cohorts created in table main.cohort trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB Initiating cluster consisting only of main thread Generating cohort set took 0.73 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Generating sample set took 0.75 secs Generating sample set took 0.26 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Generating sample set took 0.34 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Initiating cluster consisting only of main thread Generating cohort set took 0.67 secs Initiating cluster consisting only of main thread Generating cohort set took 0.59 secs Initiating cluster consisting only of main thread Generating cohort set took 0.72 secs Initiating cluster consisting only of main thread Generating cohort set took 0.71 secs Initiating cluster consisting only of main thread Generating cohort set took 0.61 secs Initiating cluster consisting only of main thread Generating cohort set took 0.64 secs Generating negative control outcomes set took 0.06 secs Generating negative control outcomes set took 0.09 secs Negative control set skipped Generating negative control outcomes set took 0.09 secs Negative control set skipped Generating negative control outcomes set took 0.06 secs Negative control set skipped trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/postgresqlV42.2.18.zip' Content type 'application/zip' length 931791 bytes (909 KB) ================================================== downloaded 909 KB Initiating cluster consisting only of main thread Generating cohort set took 0.68 secs Generating negative control outcomes set took 0.08 secs Initiating cluster consisting only of main thread Generating cohort set took 0.63 secs Generating negative control outcomes set took 0.07 secs Initiating cluster consisting only of main thread Generating cohort set took 0.67 secs Generating negative control outcomes set took 0.08 secs Initiating cluster consisting only of main thread Generating cohort set took 1.44 secs Initiating cluster consisting only of main thread Generating cohort set took 0.43 secs Initiating cluster consisting only of main thread Generating cohort set took 0.84 secs trying URL 'https://storage.googleapis.com/simba-bq-release/jdbc/SimbaBigQueryJDBC42-1.3.2.1003.zip' Content type 'application/x-zip-compressed' length 36321711 bytes (34.6 MB) ================================================== downloaded 34.6 MB [1] "Testing bigquery" [ FAIL 4 | WARN 0 | SKIP 0 | PASS 405 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-ResultsDataModel.R:84:3'): Create schema ─────────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─CohortGenerator (local) testCreateSchema(...) at test-ResultsDataModel.R:84:3 2. └─DatabaseConnector::connect(connectionDetails) at test-ResultsDataModel.R:52:3 3. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 4. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 5. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-ResultsDataModel.R:140:3'): Results upload ───────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─CohortGenerator (local) testUploadResults(...) at test-ResultsDataModel.R:140:3 2. └─CohortGenerator::uploadResults(...) at test-ResultsDataModel.R:95:3 3. └─ResultModelManager::uploadResults(...) 4. └─DatabaseConnector::connect(connectionDetails) 5. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 6. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 7. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-dbms-platforms.R:97:7'): platform specific create cohorts with stats, Incremental, get results ── Error in `paste0("jdbc:BQDriver:", connectionDetails$server)`: cannot coerce type 'closure' to vector of type 'character' Backtrace: ▆ 1. └─CohortGenerator (local) testPlatform(dbmsDetails) at test-dbms-platforms.R:97:7 2. └─CohortGenerator::runCohortGeneration(...) at test-dbms-platforms.R:56:3 3. └─DatabaseConnector::connect(connectionDetails) 4. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 5. └─DatabaseConnector:::connectBigQuery(connectionDetails) 6. └─base::paste0("jdbc:BQDriver:", connectionDetails$server) ── Error ('test-dbms-platforms.R:97:7'): platform specific create cohorts with stats, Incremental, get results ── Error in `paste0("jdbc:BQDriver:", connectionDetails$server)`: cannot coerce type 'closure' to vector of type 'character' Backtrace: ▆ 1. └─CohortGenerator (local) testPlatform(dbmsDetails) at test-dbms-platforms.R:97:7 2. └─CohortGenerator::dropCohortStatsTables(...) at test-dbms-platforms.R:8:5 3. └─DatabaseConnector::connect(connectionDetails) 4. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 5. └─DatabaseConnector:::connectBigQuery(connectionDetails) 6. └─base::paste0("jdbc:BQDriver:", connectionDetails$server) [ FAIL 4 | WARN 0 | SKIP 0 | PASS 405 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Connecting using PostgreSQL driver Error in `connectPostgreSql()`: ! Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. ├─testthat::test_check("CohortGenerator") 2. │ └─testthat::test_dir(...) 3. │ └─testthat:::test_files(...) 4. │ └─testthat:::test_files_serial(...) 5. │ └─withr (local) ``() 6. └─DatabaseConnector::connect(connectionDetails = postgresConnectionDetails) at test-ResultsDataModel.R:37:5 7. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 8. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 9. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") Execution halted