CRAN Package Check Results for Maintainer Katy Sadowski <sadowski at ohdsi.org>

CRAN Package Check Results for Maintainer ‘Katy Sadowski <sadowski at ohdsi.org>’

Last updated on 2026-05-04 00:50:34 CEST.

Package	ERROR	OK
DataQualityDashboard	2	11

Version: 2.8.7
Check: tests
Result: ERROR Running ‘testthat.R’ [51s/122s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(DataQualityDashboard) Loading required package: DatabaseConnector > > test_check("DataQualityDashboard") Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'` to /data/gannet/ripley/.Renviron and restarting R. trying URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar' Content type 'application/java-archive' length 1089312 bytes (1.0 MB) ================================================== downloaded 1.0 MB DatabaseConnector postgresql JDBC driver downloaded to '/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'` to /data/gannet/ripley/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/sqlServerV9.2.0.zip' Content type 'application/x-zip-compressed' length 1262814 bytes (1.2 MB) ================================================== downloaded 1.2 MB DatabaseConnector sql server JDBC driver downloaded to '/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'` to /data/gannet/ripley/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/oracleV19.8.zip' Content type 'application/x-zip-compressed' length 4101479 bytes (3.9 MB) ================================================== downloaded 3.9 MB DatabaseConnector oracle JDBC driver downloaded to '/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'` to /data/gannet/ripley/.Renviron and restarting R. trying URL 'https://s3.amazonaws.com/redshift-downloads/drivers/jdbc/2.1.0.20/redshift-jdbc42-2.1.0.20.zip' Content type 'application/zip' length 8434563 bytes (8.0 MB) ================================================== downloaded 8.0 MB DatabaseConnector redshift JDBC driver downloaded to '/tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/jdbcDriverscf3b65a7ac469'. 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: /tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/GiBleed_5.3.zip to: /tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/GiBleed_5.3.sqlite Connecting using SQLite driver Executing SQL took 0.0216 secs Connecting using SQLite driver 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) -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-69.R Connecting using SQLite driver Executing SQL took 0.106 secs Executing SQL took 0.0148 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-103.R Connecting using SQLite driver Executing SQL took 0.145 secs Executing SQL took 0.0414 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-140.R Connecting using SQLite driver Executing SQL took 0.0414 secs Executing SQL took 0.0296 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-177.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-convertResultsCase-23.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-23.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-47.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmField [Level: FIELD] [Check: cdmField] [CDM Table: CARE_SITE] [CDM Field: CARE_SITE_ID] row names contain missing values Saving _problems/test-executeDqChecks-71.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: plausibleGender [Level: CONCEPT] [Check: plausibleGender] [CDM Table: CONDITION_OCCURRENCE] [CDM Field: CONDITION_CONCEPT_ID] Error executing SQL: near ",": syntax error An error report has been created at /tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/dqd_cf3b641625592/errors/CONCEPT_plausibleGender_CONDITION_OCCURRENCE_CONDITION_CONCEPT_ID.txt Processing check description: plausibleUnitConceptIds Writing results to file: /tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/dqd_cf3b641625592/synthea-20260503152524.json Execution Complete Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measureObservationPeriodOverlap [Level: TABLE] [Check: measureObservationPeriodOverlap] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-122.R Connecting using SQLite driver | | | 0% | |======================================================================| 100% Executing SQL took 0.0356 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-270.R [1] "Processing database type: oracle" [1] "No connection details found for oracle, skipping..." [1] "Processing database type: postgresql" [1] "No connection details found for postgresql, skipping..." [1] "Processing database type: sql server" [1] "No connection details found for sql server, skipping..." [1] "Processing database type: redshift" [1] "No connection details found for redshift, skipping..." [1] "Processing database type: iris" [1] "No connection details found for iris, skipping..." [1] "Processing database type: snowflake" [1] "No connection details found for snowflake, skipping..." [1] "Processing database type: spark" [1] "No connection details found for spark, skipping..." [1] "Processing database type: bigquery" [1] "No connection details found for bigquery, skipping..." Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-473.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness Saving _problems/test-executeDqChecks-505.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness Saving _problems/test-executeDqChecks-538.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness Saving _problems/test-executeDqChecks-603.R Connecting using SQLite driver | | | 0% | |======================================================================| 100% Executing SQL took 0.00994 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-640.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-671.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-695.R 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: /tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/GiBleed_5.3.zip to: /tmp/RtmpcEQWYE/working_dir/RtmpF8QPrK/GiBleed_5.3_1.5.duckdb Connecting using DuckDB driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-735.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) Connecting using SQLite driver Executing SQL took 0.0351 secs Executing SQL took 0.0339 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: plausibleAfterBirth [Level: FIELD] [Check: plausibleAfterBirth] [CDM Table: CONDITION_ERA] [CDM Field: CONDITION_ERA_START_DATE] row names contain missing values Saving _problems/test-plausibleAfterBirth-45.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-reEvaluateThresholds-22.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-writeDBResultsTo-30.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-writeJsonResultsTo-22.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-writeJsonResultsTo-68.R [ FAIL 23 | WARN 0 | SKIP 3 | PASS 28 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-executeDqChecks.R:547:1' • empty test (2): 'test-executeDqChecks.R:280:1', ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-calculateNotApplicableStatus.R:52:3'): Not Applicable status Table Empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:52:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-calculateNotApplicableStatus.R:86:3'): measureConditionEraCompleteness Not Applicable if condition_occurrence empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:86:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-calculateNotApplicableStatus.R:123:3'): measureConditionEraCompleteness Fails if condition_era empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:123:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-calculateNotApplicableStatus.R:160:3'): measurePersonCompleteness NOT marked as Not Applicable when table is empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:160:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-convertResultsCase.R:7:3'): Camel correctly converted to snake and back ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-convertResultsCase.R:7:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:8:3'): Execute a single DQ check on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:8:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:32:3'): Execute all TABLE checks on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:32:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:56:3'): Execute FIELD checks on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:56:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:107:3'): Execute observation period overlap check ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:107:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:253:3'): Execute a single DQ check on a cohort in Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:253:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:457:3'): Execute DQ checks and write to table ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:457:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:486:3'): Execute DQ checks using sqlOnly=TRUE and sqlOnlyUnionCount=4 and sqlOnlyIncrementalInsert=TRUE ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:486:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.createSqlOnlyQueries(...) 9. └─DataQualityDashboard:::.recordResult(...) 10. └─base::data.frame(...) 11. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 12. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 13. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:519:3'): Execute DQ checks using sqlOnly=TRUE and sqlOnlyUnionCount=1 and sqlOnlyIncrementalInsert=TRUE ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:519:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.createSqlOnlyQueries(...) 9. └─DataQualityDashboard:::.recordResult(...) 10. └─base::data.frame(...) 11. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 12. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 13. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:584:3'): Incremental insert SQL is valid. ──── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:584:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.createSqlOnlyQueries(...) 9. └─DataQualityDashboard:::.recordResult(...) 10. └─base::data.frame(...) 11. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 12. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 13. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:630:3'): Multiple cdm_source rows triggers warning. ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─testthat::capture_warnings(...) at test-executeDqChecks.R:630:3 2. │ └─base::withCallingHandlers(...) 3. └─DataQualityDashboard::executeDqChecks(...) 4. └─ParallelLogger::clusterApply(...) 5. └─base::lapply(x, fun, ...) 6. └─DataQualityDashboard (local) FUN(X[[i]], ...) 7. └─base::apply(...) 8. └─DataQualityDashboard (local) FUN(newX[, i], ...) 9. └─DataQualityDashboard:::.processCheck(...) 10. └─base::tryCatch(...) 11. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. └─base (local) tryCatchOne(...) 13. └─value[[3L]](cond) 14. └─DataQualityDashboard:::.recordResult(...) 15. └─base::data.frame(...) 16. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 18. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:651:3'): Execute checks on Synthea/Eunomia to test new variable executionTimeSeconds ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:651:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:680:3'): checkNames are filtered by checkSeverity ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:680:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:720:3'): Execute a single DQ check on DuckDB ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:720:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-plausibleAfterBirth.R:29:3'): plausibleAfterBirth allows events on same day as birth (issue #561) ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-plausibleAfterBirth.R:29:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-reEvaluateThresholds.R:7:3'): Execute reEvaluateThresholds on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-reEvaluateThresholds.R:7:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-writeDBResultsTo.R:12:3'): Write DB results to json ──────────── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-writeDBResultsTo.R:12:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-writeJsonResultsTo.R:7:3'): Write JSON results ───────────────── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-writeJsonResultsTo.R:7:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-writeJsonResultsTo.R:53:3'): Write JSON results with singleTable parameter ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-writeJsonResultsTo.R:53:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) [ FAIL 23 | WARN 0 | SKIP 3 | PASS 28 ] Error: ! Test failures. Warning message: call dbDisconnect() when finished working with a connection Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.8.7
Check: tests
Result: ERROR Running 'testthat.R' [50s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(DataQualityDashboard) Loading required package: DatabaseConnector > > test_check("DataQualityDashboard") Consider adding `DATABASECONNECTOR_JAR_FOLDER='D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'` to C:\Users\CRAN\Documents/.Renviron and restarting R. trying URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar' Content type 'application/java-archive' length 1089312 bytes (1.0 MB) ================================================== downloaded 1.0 MB DatabaseConnector postgresql JDBC driver downloaded to 'D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'` to C:\Users\CRAN\Documents/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/sqlServerV9.2.0.zip' Content type 'application/x-zip-compressed' length 1262814 bytes (1.2 MB) ================================================== downloaded 1.2 MB DatabaseConnector sql server JDBC driver downloaded to 'D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'` to C:\Users\CRAN\Documents/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/oracleV19.8.zip' Content type 'application/x-zip-compressed' length 4101479 bytes (3.9 MB) ================================================== downloaded 3.9 MB DatabaseConnector oracle JDBC driver downloaded to 'D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'` to C:\Users\CRAN\Documents/.Renviron and restarting R. trying URL 'https://s3.amazonaws.com/redshift-downloads/drivers/jdbc/2.1.0.20/redshift-jdbc42-2.1.0.20.zip' Content type 'application/zip' length 8434563 bytes (8.0 MB) ================================================== downloaded 8.0 MB DatabaseConnector redshift JDBC driver downloaded to 'D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\jdbcDrivers1497c7e9e27f'. 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\2026_04_30_01_50_01_32376\RtmpCG4GuC/GiBleed_5.3.zip to: D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC/GiBleed_5.3.sqlite Connecting using SQLite driver Executing SQL took 0.0101 secs Connecting using SQLite driver 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) -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-69.R Connecting using SQLite driver Executing SQL took 0.0715 secs Executing SQL took 0.0137 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-103.R Connecting using SQLite driver Executing SQL took 0.0341 secs Executing SQL took 0.0102 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-140.R Connecting using SQLite driver Executing SQL took 0.00844 secs Executing SQL took 0.00677 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-calculateNotApplicableStatus-177.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-convertResultsCase-23.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-23.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-47.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmField [Level: FIELD] [Check: cdmField] [CDM Table: CARE_SITE] [CDM Field: CARE_SITE_ID] row names contain missing values Saving _problems/test-executeDqChecks-71.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: plausibleGender [Level: CONCEPT] [Check: plausibleGender] [CDM Table: CONDITION_OCCURRENCE] [CDM Field: CONDITION_CONCEPT_ID] Error executing SQL: near ",": syntax error An error report has been created at D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\dqd_1497c3a84263d/errors/CONCEPT_plausibleGender_CONDITION_OCCURRENCE_CONDITION_CONCEPT_ID.txt Processing check description: plausibleUnitConceptIds Writing results to file: D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC\dqd_1497c3a84263d/synthea-20260430083938.json Execution Complete Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measureObservationPeriodOverlap [Level: TABLE] [Check: measureObservationPeriodOverlap] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-122.R Connecting using SQLite driver | | | 0% | |======================================================================| 100% Executing SQL took 0.00693 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-270.R [1] "Processing database type: oracle" [1] "No connection details found for oracle, skipping..." [1] "Processing database type: postgresql" [1] "No connection details found for postgresql, skipping..." [1] "Processing database type: sql server" [1] "No connection details found for sql server, skipping..." [1] "Processing database type: redshift" [1] "No connection details found for redshift, skipping..." [1] "Processing database type: iris" [1] "No connection details found for iris, skipping..." [1] "Processing database type: snowflake" [1] "No connection details found for snowflake, skipping..." [1] "Processing database type: spark" [1] "No connection details found for spark, skipping..." [1] "Processing database type: bigquery" [1] "No connection details found for bigquery, skipping..." Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-473.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness Saving _problems/test-executeDqChecks-505.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness Saving _problems/test-executeDqChecks-538.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness Saving _problems/test-executeDqChecks-603.R Connecting using SQLite driver | | | 0% | |======================================================================| 100% Executing SQL took 0.00594 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-640.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-671.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: cdmTable [Level: TABLE] [Check: cdmTable] [CDM Table: PERSON] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-695.R 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\2026_04_30_01_50_01_32376\RtmpCG4GuC/GiBleed_5.3.zip to: D:\temp\2026_04_30_01_50_01_32376\RtmpCG4GuC/GiBleed_5.3_1.5.duckdb Connecting using DuckDB driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-executeDqChecks-735.R -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) Connecting using SQLite driver Executing SQL took 0.00943 secs Executing SQL took 0.00962 secs Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: COST, CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: plausibleAfterBirth [Level: FIELD] [Check: plausibleAfterBirth] [CDM Table: CONDITION_ERA] [CDM Field: CONDITION_ERA_START_DATE] row names contain missing values Saving _problems/test-plausibleAfterBirth-45.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-reEvaluateThresholds-22.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-writeDBResultsTo-30.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-writeJsonResultsTo-22.R Connecting using SQLite driver -- Column specification -------------------------------------------------------- cols( checkLevel = col_character(), checkName = col_character(), checkDescription = col_character(), kahnContext = col_character(), kahnCategory = col_character(), kahnSubcategory = col_character(), sqlFile = col_character(), evaluationFilter = col_character(), severity = col_character() ) CDM Tables skipped: CONCEPT, VOCABULARY, CONCEPT_ANCESTOR, CONCEPT_RELATIONSHIP, CONCEPT_CLASS, CONCEPT_SYNONYM, RELATIONSHIP, DOMAIN Processing check description: measurePersonCompleteness [Level: TABLE] [Check: measurePersonCompleteness] [CDM Table: OBSERVATION_PERIOD] [CDM Field: NA] row names contain missing values Saving _problems/test-writeJsonResultsTo-68.R [ FAIL 23 | WARN 0 | SKIP 3 | PASS 28 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-executeDqChecks.R:547:1' • empty test (2): 'test-executeDqChecks.R:280:1', ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-calculateNotApplicableStatus.R:52:3'): Not Applicable status Table Empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:52:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-calculateNotApplicableStatus.R:86:3'): measureConditionEraCompleteness Not Applicable if condition_occurrence empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:86:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-calculateNotApplicableStatus.R:123:3'): measureConditionEraCompleteness Fails if condition_era empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:123:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-calculateNotApplicableStatus.R:160:3'): measurePersonCompleteness NOT marked as Not Applicable when table is empty ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-calculateNotApplicableStatus.R:160:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-convertResultsCase.R:7:3'): Camel correctly converted to snake and back ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-convertResultsCase.R:7:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:8:3'): Execute a single DQ check on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:8:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:32:3'): Execute all TABLE checks on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:32:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:56:3'): Execute FIELD checks on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:56:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:107:3'): Execute observation period overlap check ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:107:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:253:3'): Execute a single DQ check on a cohort in Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:253:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:457:3'): Execute DQ checks and write to table ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:457:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:486:3'): Execute DQ checks using sqlOnly=TRUE and sqlOnlyUnionCount=4 and sqlOnlyIncrementalInsert=TRUE ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:486:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.createSqlOnlyQueries(...) 9. └─DataQualityDashboard:::.recordResult(...) 10. └─base::data.frame(...) 11. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 12. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 13. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:519:3'): Execute DQ checks using sqlOnly=TRUE and sqlOnlyUnionCount=1 and sqlOnlyIncrementalInsert=TRUE ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:519:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.createSqlOnlyQueries(...) 9. └─DataQualityDashboard:::.recordResult(...) 10. └─base::data.frame(...) 11. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 12. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 13. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:584:3'): Incremental insert SQL is valid. ──── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:584:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.createSqlOnlyQueries(...) 9. └─DataQualityDashboard:::.recordResult(...) 10. └─base::data.frame(...) 11. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 12. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 13. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:630:3'): Multiple cdm_source rows triggers warning. ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─testthat::capture_warnings(...) at test-executeDqChecks.R:630:3 2. │ └─base::withCallingHandlers(...) 3. └─DataQualityDashboard::executeDqChecks(...) 4. └─ParallelLogger::clusterApply(...) 5. └─base::lapply(x, fun, ...) 6. └─DataQualityDashboard (local) FUN(X[[i]], ...) 7. └─base::apply(...) 8. └─DataQualityDashboard (local) FUN(newX[, i], ...) 9. └─DataQualityDashboard:::.processCheck(...) 10. └─base::tryCatch(...) 11. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. └─base (local) tryCatchOne(...) 13. └─value[[3L]](cond) 14. └─DataQualityDashboard:::.recordResult(...) 15. └─base::data.frame(...) 16. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 18. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:651:3'): Execute checks on Synthea/Eunomia to test new variable executionTimeSeconds ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:651:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:680:3'): checkNames are filtered by checkSeverity ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:680:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-executeDqChecks.R:720:3'): Execute a single DQ check on DuckDB ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-executeDqChecks.R:720:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-plausibleAfterBirth.R:29:3'): plausibleAfterBirth allows events on same day as birth (issue #561) ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-plausibleAfterBirth.R:29:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-reEvaluateThresholds.R:7:3'): Execute reEvaluateThresholds on Synthea/Eunomia ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-reEvaluateThresholds.R:7:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-writeDBResultsTo.R:12:3'): Write DB results to json ──────────── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-writeDBResultsTo.R:12:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-writeJsonResultsTo.R:7:3'): Write JSON results ───────────────── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-writeJsonResultsTo.R:7:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) ── Error ('test-writeJsonResultsTo.R:53:3'): Write JSON results with singleTable parameter ── Error in `as.data.frame.vector(x, ..., nm = nm)`: row names contain missing values Backtrace: ▆ 1. ├─base::withCallingHandlers(...) at test-writeJsonResultsTo.R:53:3 2. └─DataQualityDashboard::executeDqChecks(...) 3. └─ParallelLogger::clusterApply(...) 4. └─base::lapply(x, fun, ...) 5. └─DataQualityDashboard (local) FUN(X[[i]], ...) 6. └─base::apply(...) 7. └─DataQualityDashboard (local) FUN(newX[, i], ...) 8. └─DataQualityDashboard:::.processCheck(...) 9. └─base::tryCatch(...) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(...) 12. └─value[[3L]](cond) 13. └─DataQualityDashboard:::.recordResult(...) 14. └─base::data.frame(...) 15. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 16. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) 17. └─base::as.data.frame.vector(x, ..., nm = nm) [ FAIL 23 | WARN 0 | SKIP 3 | PASS 28 ] Error: ! Test failures. Warning message: call dbDisconnect() when finished working with a connection Execution halted Flavor: r-devel-windows-x86_64

CRAN Package Check Results for Maintainer ‘Katy Sadowski <sadowski at ohdsi.org>’

Package DataQualityDashboard

Additional issues