CRAN Package Check Results for Package Eunomia

Last updated on 2026-10-11 04:50:57 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.1.0	5.48	97.45	102.93	OK
r-devel-linux-x86_64-debian-gcc	2.1.0	3.52	43.62	47.14	ERROR
r-devel-linux-x86_64-fedora-clang	2.1.0			42.07	ERROR
r-devel-linux-x86_64-fedora-gcc	2.1.0			45.05	ERROR
r-devel-windows-x86_64	2.1.0	8.00	165.00	173.00	OK
r-patched-linux-x86_64	2.1.0	5.70	126.25	131.95	OK
r-release-linux-x86_64	2.1.0	5.19	52.23	57.42	ERROR
r-release-macos-arm64	2.1.0	2.00	45.00	47.00	OK
r-release-macos-x86_64	2.1.0	4.00	155.00	159.00	OK
r-release-windows-x86_64	2.1.0	8.00	161.00	169.00	OK
r-oldrel-macos-arm64	2.1.0				OK
r-oldrel-macos-x86_64	2.1.0	3.00	88.00	91.00	OK
r-oldrel-windows-x86_64	2.1.0	9.00	187.00	196.00	OK

Check Details

Version: 2.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Eunomia) > test_check("Eunomia") 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 Saving _problems/test-DBI-2.R 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 Saving _problems/test-DBI-13.R 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 trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/Synthea27Nj/Synthea27Nj_5.4.zip' Content type 'application/zip' length 3351707 bytes (3.2 MB) ================================================== downloaded 3.2 MB Saving _problems/test-EunomiaData-14.R adding: home/hornik/tmp/scratch/RtmpLQiXOr/file263a582834cee6somefile.txt (stored 0%) 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 Saving _problems/test-basic-9.R 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 Saving _problems/test-basic-17.R Saving _problems/test-basic-49.R Cohorts created in table main.cohort Saving _problems/test-basic-62.R Cohorts created in table main.cohort [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-DBI.R:2:3'): dbConnect works with sqlite ─────────────────────── Error: not an error Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:2:3 2. ├─DBI::dbConnect(...) 3. │ └─RSQLite (local) .local(drv, ...) 4. │ └─base::stopifnot(length(dbname) == 1, !is.na(dbname)) 5. └─Eunomia::getDatabaseFile(...) 6. └─Eunomia::extractLoadData(...) 7. └─Eunomia::loadDataFiles(...) 8. ├─DBI::dbExecute(conn = connection, statement = statement) 9. └─DBI::dbExecute(conn = connection, statement = statement) 10. ├─DBI::dbSendStatement(conn, statement, ...) 11. └─DBI::dbSendStatement(conn, statement, ...) 12. ├─DBI::dbSendQuery(conn, statement, ...) 13. └─RSQLite::dbSendQuery(conn, statement, ...) 14. └─RSQLite (local) .local(conn, statement, ...) 15. ├─methods::new(...) 16. │ ├─methods::initialize(value, ...) 17. │ └─methods::initialize(value, ...) 18. └─RSQLite:::result_create(conn@ptr, statement) ── Error ('test-DBI.R:13:3'): dbConnect works with duckdb ────────────────────── <duckdb_error/rlang_error/error/condition> Error in `dbSendQuery(conn, statement, ...)`: No statements to execute ℹ Context: rapi_prepare Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:13:3 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─Eunomia::getDatabaseFile(...) 6. │ └─Eunomia::extractLoadData(...) 7. │ └─Eunomia::loadDataFiles(...) 8. │ ├─DBI::dbExecute(conn = connection, statement = statement) 9. │ └─DBI::dbExecute(conn = connection, statement = statement) 10. │ ├─DBI::dbSendStatement(conn, statement, ...) 11. │ └─DBI::dbSendStatement(conn, statement, ...) 12. │ ├─DBI::dbSendQuery(conn, statement, ...) 13. │ └─duckdb::dbSendQuery(conn, statement, ...) 14. │ └─duckdb (local) .local(conn, statement, ...) 15. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 16. │ ├─rlang::try_fetch(...) 17. │ │ ├─base::tryCatch(...) 18. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 19. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 21. │ │ └─base::withCallingHandlers(...) 22. │ └─duckdb:::rapi_prepare(conn, query, env) 23. ├─duckdb (local) `<fn>`("rapi_prepare", "No statements to execute") 24. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) 25. │ └─rlang:::signal_abort(cnd, .file) 26. │ └─base::signalCondition(cnd) 27. └─rlang (local) `<fn>`(`<dckdb_rr>`) 28. └─handlers[[1L]](cnd) 29. └─duckdb:::rethrow_error_from_rapi(e, call) 30. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields) ── Error ('test-EunomiaData.R:14:3'): Eunomia works with 5.4 ─────────────────── Error: not an error Backtrace: ▆ 1. └─Eunomia::getDatabaseFile(...) at test-EunomiaData.R:14:3 2. └─Eunomia::extractLoadData(...) 3. └─Eunomia::loadDataFiles(...) 4. ├─DBI::dbExecute(conn = connection, statement = statement) 5. └─DBI::dbExecute(conn = connection, statement = statement) 6. ├─DBI::dbSendStatement(conn, statement, ...) 7. └─DBI::dbSendStatement(conn, statement, ...) 8. ├─DBI::dbSendQuery(conn, statement, ...) 9. └─RSQLite::dbSendQuery(conn, statement, ...) 10. └─RSQLite (local) .local(conn, statement, ...) 11. ├─methods::new(...) 12. │ ├─methods::initialize(value, ...) 13. │ └─methods::initialize(value, ...) 14. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:9:3'): Dataset not downloaded and not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:9:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:17:3'): Dataset downloaded but not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:17:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:49:3'): Query ──────────────────────────────────────── Expected `personCount` > 0. Actual comparison: "0" <= "0" ── Failure ('test-basic.R:62:3'): Cohort construction ────────────────────────── Expected `cohortCount` > 0. Actual comparison: "0" <= "0" [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] Error: ! Test failures. Warning message: call dbDisconnect() when finished working with a connection Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/10s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Eunomia) > test_check("Eunomia") 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 Saving _problems/test-DBI-2.R 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 Saving _problems/test-DBI-13.R 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 trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/Synthea27Nj/Synthea27Nj_5.4.zip' Content type 'application/zip' length 3351707 bytes (3.2 MB) ================================================== downloaded 3.2 MB Saving _problems/test-EunomiaData-14.R adding: tmp/RtmpzCKMPa/working_dir/RtmpWq1Hrv/file6cf1b68ee78b0somefile.txt (stored 0%) 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 Saving _problems/test-basic-9.R 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 Saving _problems/test-basic-17.R Saving _problems/test-basic-49.R Cohorts created in table main.cohort Saving _problems/test-basic-62.R Cohorts created in table main.cohort [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-DBI.R:2:3'): dbConnect works with sqlite ─────────────────────── Error: not an error Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:2:3 2. ├─DBI::dbConnect(...) 3. │ └─RSQLite (local) .local(drv, ...) 4. │ └─base::stopifnot(length(dbname) == 1, !is.na(dbname)) 5. └─Eunomia::getDatabaseFile(...) 6. └─Eunomia::extractLoadData(...) 7. └─Eunomia::loadDataFiles(...) 8. ├─DBI::dbExecute(conn = connection, statement = statement) 9. └─DBI::dbExecute(conn = connection, statement = statement) 10. ├─DBI::dbSendStatement(conn, statement, ...) 11. └─DBI::dbSendStatement(conn, statement, ...) 12. ├─DBI::dbSendQuery(conn, statement, ...) 13. └─RSQLite::dbSendQuery(conn, statement, ...) 14. └─RSQLite (local) .local(conn, statement, ...) 15. ├─methods::new(...) 16. │ ├─methods::initialize(value, ...) 17. │ └─methods::initialize(value, ...) 18. └─RSQLite:::result_create(conn@ptr, statement) ── Error ('test-DBI.R:13:3'): dbConnect works with duckdb ────────────────────── <duckdb_error/rlang_error/error/condition> Error in `dbSendQuery(conn, statement, ...)`: No statements to execute ℹ Context: rapi_prepare Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:13:3 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─Eunomia::getDatabaseFile(...) 6. │ └─Eunomia::extractLoadData(...) 7. │ └─Eunomia::loadDataFiles(...) 8. │ ├─DBI::dbExecute(conn = connection, statement = statement) 9. │ └─DBI::dbExecute(conn = connection, statement = statement) 10. │ ├─DBI::dbSendStatement(conn, statement, ...) 11. │ └─DBI::dbSendStatement(conn, statement, ...) 12. │ ├─DBI::dbSendQuery(conn, statement, ...) 13. │ └─duckdb::dbSendQuery(conn, statement, ...) 14. │ └─duckdb (local) .local(conn, statement, ...) 15. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 16. │ ├─rlang::try_fetch(...) 17. │ │ ├─base::tryCatch(...) 18. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 19. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 21. │ │ └─base::withCallingHandlers(...) 22. │ └─duckdb:::rapi_prepare(conn, query, env) 23. ├─duckdb (local) `<fn>`("rapi_prepare", "No statements to execute") 24. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) 25. │ └─rlang:::signal_abort(cnd, .file) 26. │ └─base::signalCondition(cnd) 27. └─rlang (local) `<fn>`(`<dckdb_rr>`) 28. └─handlers[[1L]](cnd) 29. └─duckdb:::rethrow_error_from_rapi(e, call) 30. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields) ── Error ('test-EunomiaData.R:14:3'): Eunomia works with 5.4 ─────────────────── Error: not an error Backtrace: ▆ 1. └─Eunomia::getDatabaseFile(...) at test-EunomiaData.R:14:3 2. └─Eunomia::extractLoadData(...) 3. └─Eunomia::loadDataFiles(...) 4. ├─DBI::dbExecute(conn = connection, statement = statement) 5. └─DBI::dbExecute(conn = connection, statement = statement) 6. ├─DBI::dbSendStatement(conn, statement, ...) 7. └─DBI::dbSendStatement(conn, statement, ...) 8. ├─DBI::dbSendQuery(conn, statement, ...) 9. └─RSQLite::dbSendQuery(conn, statement, ...) 10. └─RSQLite (local) .local(conn, statement, ...) 11. ├─methods::new(...) 12. │ ├─methods::initialize(value, ...) 13. │ └─methods::initialize(value, ...) 14. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:9:3'): Dataset not downloaded and not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:9:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:17:3'): Dataset downloaded but not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:17:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:49:3'): Query ──────────────────────────────────────── Expected `personCount` > 0. Actual comparison: "0" <= "0" ── Failure ('test-basic.R:62:3'): Cohort construction ────────────────────────── Expected `cohortCount` > 0. Actual comparison: "0" <= "0" [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [13s/14s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Eunomia) > test_check("Eunomia") 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 Saving _problems/test-DBI-2.R 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 Saving _problems/test-DBI-13.R 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 trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/Synthea27Nj/Synthea27Nj_5.4.zip' Content type 'application/zip' length 3351707 bytes (3.2 MB) ================================================== downloaded 3.2 MB Saving _problems/test-EunomiaData-14.R adding: tmp/RtmplRIC6I/working_dir/RtmpbiUQp2/file654af49d96fdbsomefile.txt (stored 0%) 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 Saving _problems/test-basic-9.R 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 Saving _problems/test-basic-17.R Saving _problems/test-basic-49.R Cohorts created in table main.cohort Saving _problems/test-basic-62.R Cohorts created in table main.cohort [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-DBI.R:2:3'): dbConnect works with sqlite ─────────────────────── Error: not an error Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:2:3 2. ├─DBI::dbConnect(...) 3. │ └─RSQLite (local) .local(drv, ...) 4. │ └─base::stopifnot(length(dbname) == 1, !is.na(dbname)) 5. └─Eunomia::getDatabaseFile(...) 6. └─Eunomia::extractLoadData(...) 7. └─Eunomia::loadDataFiles(...) 8. ├─DBI::dbExecute(conn = connection, statement = statement) 9. └─DBI::dbExecute(conn = connection, statement = statement) 10. ├─DBI::dbSendStatement(conn, statement, ...) 11. └─DBI::dbSendStatement(conn, statement, ...) 12. ├─DBI::dbSendQuery(conn, statement, ...) 13. └─RSQLite::dbSendQuery(conn, statement, ...) 14. └─RSQLite (local) .local(conn, statement, ...) 15. ├─methods::new(...) 16. │ ├─methods::initialize(value, ...) 17. │ └─methods::initialize(value, ...) 18. └─RSQLite:::result_create(conn@ptr, statement) ── Error ('test-DBI.R:13:3'): dbConnect works with duckdb ────────────────────── <duckdb_error/rlang_error/error/condition> Error in `dbSendQuery(conn, statement, ...)`: No statements to execute ℹ Context: rapi_prepare Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:13:3 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─Eunomia::getDatabaseFile(...) 6. │ └─Eunomia::extractLoadData(...) 7. │ └─Eunomia::loadDataFiles(...) 8. │ ├─DBI::dbExecute(conn = connection, statement = statement) 9. │ └─DBI::dbExecute(conn = connection, statement = statement) 10. │ ├─DBI::dbSendStatement(conn, statement, ...) 11. │ └─DBI::dbSendStatement(conn, statement, ...) 12. │ ├─DBI::dbSendQuery(conn, statement, ...) 13. │ └─duckdb::dbSendQuery(conn, statement, ...) 14. │ └─duckdb (local) .local(conn, statement, ...) 15. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 16. │ ├─rlang::try_fetch(...) 17. │ │ ├─base::tryCatch(...) 18. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 19. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 21. │ │ └─base::withCallingHandlers(...) 22. │ └─duckdb:::rapi_prepare(conn, query, env) 23. ├─duckdb (local) `<fn>`("rapi_prepare", "No statements to execute") 24. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) 25. │ └─rlang:::signal_abort(cnd, .file) 26. │ └─base::signalCondition(cnd) 27. └─rlang (local) `<fn>`(`<dckdb_rr>`) 28. └─handlers[[1L]](cnd) 29. └─duckdb:::rethrow_error_from_rapi(e, call) 30. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields) ── Error ('test-EunomiaData.R:14:3'): Eunomia works with 5.4 ─────────────────── Error: not an error Backtrace: ▆ 1. └─Eunomia::getDatabaseFile(...) at test-EunomiaData.R:14:3 2. └─Eunomia::extractLoadData(...) 3. └─Eunomia::loadDataFiles(...) 4. ├─DBI::dbExecute(conn = connection, statement = statement) 5. └─DBI::dbExecute(conn = connection, statement = statement) 6. ├─DBI::dbSendStatement(conn, statement, ...) 7. └─DBI::dbSendStatement(conn, statement, ...) 8. ├─DBI::dbSendQuery(conn, statement, ...) 9. └─RSQLite::dbSendQuery(conn, statement, ...) 10. └─RSQLite (local) .local(conn, statement, ...) 11. ├─methods::new(...) 12. │ ├─methods::initialize(value, ...) 13. │ └─methods::initialize(value, ...) 14. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:9:3'): Dataset not downloaded and not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:9:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:17:3'): Dataset downloaded but not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:17:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:49:3'): Query ──────────────────────────────────────── Expected `personCount` > 0. Actual comparison: "0" <= "0" ── Failure ('test-basic.R:62:3'): Cohort construction ────────────────────────── Expected `cohortCount` > 0. Actual comparison: "0" <= "0" [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] Error: ! Test failures. Warning message: call dbDisconnect() when finished working with a connection Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/15s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Eunomia) > test_check("Eunomia") 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 Saving _problems/test-DBI-2.R 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 Saving _problems/test-DBI-13.R 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 trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/Synthea27Nj/Synthea27Nj_5.4.zip' Content type 'application/zip' length 3351707 bytes (3.2 MB) ================================================== downloaded 3.2 MB Saving _problems/test-EunomiaData-14.R adding: home/hornik/tmp/scratch/RtmprG9Fa0/filef356479ffaeffsomefile.txt (stored 0%) 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 Saving _problems/test-basic-9.R 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 Saving _problems/test-basic-17.R Saving _problems/test-basic-49.R Cohorts created in table main.cohort Saving _problems/test-basic-62.R Cohorts created in table main.cohort [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-DBI.R:2:3'): dbConnect works with sqlite ─────────────────────── Error: not an error Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:2:3 2. ├─DBI::dbConnect(...) 3. │ └─RSQLite (local) .local(drv, ...) 4. │ └─base::stopifnot(length(dbname) == 1, !is.na(dbname)) 5. └─Eunomia::getDatabaseFile(...) 6. └─Eunomia::extractLoadData(...) 7. └─Eunomia::loadDataFiles(...) 8. ├─DBI::dbExecute(conn = connection, statement = statement) 9. └─DBI::dbExecute(conn = connection, statement = statement) 10. ├─DBI::dbSendStatement(conn, statement, ...) 11. └─DBI::dbSendStatement(conn, statement, ...) 12. ├─DBI::dbSendQuery(conn, statement, ...) 13. └─RSQLite::dbSendQuery(conn, statement, ...) 14. └─RSQLite (local) .local(conn, statement, ...) 15. ├─methods::new(...) 16. │ ├─methods::initialize(value, ...) 17. │ └─methods::initialize(value, ...) 18. └─RSQLite:::result_create(conn@ptr, statement) ── Error ('test-DBI.R:13:3'): dbConnect works with duckdb ────────────────────── <duckdb_error/rlang_error/error/condition> Error in `dbSendQuery(conn, statement, ...)`: No statements to execute ℹ Context: rapi_prepare Backtrace: ▆ 1. ├─DBI::dbConnect(...) at test-DBI.R:13:3 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─Eunomia::getDatabaseFile(...) 6. │ └─Eunomia::extractLoadData(...) 7. │ └─Eunomia::loadDataFiles(...) 8. │ ├─DBI::dbExecute(conn = connection, statement = statement) 9. │ └─DBI::dbExecute(conn = connection, statement = statement) 10. │ ├─DBI::dbSendStatement(conn, statement, ...) 11. │ └─DBI::dbSendStatement(conn, statement, ...) 12. │ ├─DBI::dbSendQuery(conn, statement, ...) 13. │ └─duckdb::dbSendQuery(conn, statement, ...) 14. │ └─duckdb (local) .local(conn, statement, ...) 15. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 16. │ ├─rlang::try_fetch(...) 17. │ │ ├─base::tryCatch(...) 18. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 19. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 21. │ │ └─base::withCallingHandlers(...) 22. │ └─duckdb:::rapi_prepare(conn, query, env) 23. ├─duckdb (local) `<fn>`("rapi_prepare", "No statements to execute") 24. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) 25. │ └─rlang:::signal_abort(cnd, .file) 26. │ └─base::signalCondition(cnd) 27. └─rlang (local) `<fn>`(`<dckdb_rr>`) 28. └─handlers[[1L]](cnd) 29. └─duckdb:::rethrow_error_from_rapi(e, call) 30. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields) ── Error ('test-EunomiaData.R:14:3'): Eunomia works with 5.4 ─────────────────── Error: not an error Backtrace: ▆ 1. └─Eunomia::getDatabaseFile(...) at test-EunomiaData.R:14:3 2. └─Eunomia::extractLoadData(...) 3. └─Eunomia::loadDataFiles(...) 4. ├─DBI::dbExecute(conn = connection, statement = statement) 5. └─DBI::dbExecute(conn = connection, statement = statement) 6. ├─DBI::dbSendStatement(conn, statement, ...) 7. └─DBI::dbSendStatement(conn, statement, ...) 8. ├─DBI::dbSendQuery(conn, statement, ...) 9. └─RSQLite::dbSendQuery(conn, statement, ...) 10. └─RSQLite (local) .local(conn, statement, ...) 11. ├─methods::new(...) 12. │ ├─methods::initialize(value, ...) 13. │ └─methods::initialize(value, ...) 14. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:9:3'): Dataset not downloaded and not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:9:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:17:3'): Dataset downloaded but not loaded into SQLite ── `getDatabaseFile(datasetName = "GiBleed")` threw an error. Message: not an error Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-basic.R:17:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Eunomia::getDatabaseFile(datasetName = "GiBleed") 7. └─Eunomia::extractLoadData(...) 8. └─Eunomia::loadDataFiles(...) 9. ├─DBI::dbExecute(conn = connection, statement = statement) 10. └─DBI::dbExecute(conn = connection, statement = statement) 11. ├─DBI::dbSendStatement(conn, statement, ...) 12. └─DBI::dbSendStatement(conn, statement, ...) 13. ├─DBI::dbSendQuery(conn, statement, ...) 14. └─RSQLite::dbSendQuery(conn, statement, ...) 15. └─RSQLite (local) .local(conn, statement, ...) 16. ├─methods::new(...) 17. │ ├─methods::initialize(value, ...) 18. │ └─methods::initialize(value, ...) 19. └─RSQLite:::result_create(conn@ptr, statement) ── Failure ('test-basic.R:49:3'): Query ──────────────────────────────────────── Expected `personCount` > 0. Actual comparison: "0" <= "0" ── Failure ('test-basic.R:62:3'): Cohort construction ────────────────────────── Expected `cohortCount` > 0. Actual comparison: "0" <= "0" [ FAIL 7 | WARN 0 | SKIP 0 | PASS 54 ] Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64