• using R Under development (unstable) (2026-10-08 r90650)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)     GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-10-09 08:40:02 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘OdysseusCharacterizationModule/DESCRIPTION’ ... OK
• this is package ‘OdysseusCharacterizationModule’ version ‘0.0.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘OdysseusCharacterizationModule’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [5s/10s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [22s/42s] ERROR   Running ‘testthat.R’ [22s/41s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(OdysseusCharacterizationModule)   >   > test_check("OdysseusCharacterizationModule")   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/RtmpYIIsfy/working_dir/RtmpfNQ42U/GiBleed_5.3.zip to: /tmp/RtmpYIIsfy/working_dir/RtmpfNQ42U/GiBleed_5.3.sqlite   Saving _problems/test-covariateData-133.R   Connecting using SQLite driver   duckdb is storing downloaded extensions and secrets under ~/.duckdb:   i /data/localhost/ripley/.duckdb   This persists across sessions and is shared with the DuckDB CLI and other clients.   i Run duckdb(shared_home = FALSE) to use a temporary directory instead.   i See ?duckdb_storage for details and alternatives.   Connecting using SQLite driver   Cohorts created in table main.cohort   ▶ == Executing 1 analysis spec(s) ============================   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   ✓ Complete: 1 succeeded, 0 failed out of 1   duckdb is storing downloaded extensions and secrets under ~/.duckdb:   i /data/localhost/ripley/.duckdb   This persists across sessions and is shared with the DuckDB CLI and other clients.   i Run duckdb(shared_home = FALSE) to use a temporary directory instead.   i See ?duckdb_storage for details and alternatives.   Saving _problems/test-covariateData-323.R   Saving _problems/test-covariateData-328.R   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   Cohorts created in table main.cohort   Connecting using SQLite driver   ▶ == Executing 2 analysis spec(s) ============================   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   • Executing spec 1002: Condition occurrence [-30, -1]     ✓ 0 rows returned   ✓ Complete: 2 succeeded, 0 failed out of 2   Cohorts created in table main.cohort   Connecting using SQLite driver   ▶ == Executing 2 analysis spec(s) ============================   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   • Executing spec 9999: bad_spec   ! Spec 9999 failed: Error executing SQL:   no such table: nonexistent_table_xyz   An error report has been created at /data/localhost/ripley/R/packages/tests-devel/OdysseusCharacterizationModule.Rcheck/tests/testthat/errorReportSql.txt   ✓ Complete: 1 succeeded, 1 failed out of 2   Cohorts created in table main.cohort   Connecting using SQLite driver   ▶ == Executing 1 analysis spec(s) ============================   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   ✓ Complete: 1 succeeded, 0 failed out of 1   Cohorts created in table main.cohort   Connecting using SQLite driver   ▶ == Executing 0 analysis spec(s) ============================   ✓ Complete: 0 succeeded, 0 failed out of 0   Cohorts created in table main.cohort   Connecting using SQLite driver   ▶ == Executing 1 analysis spec(s) ============================   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   ✓ Complete: 1 succeeded, 0 failed out of 1   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Visit occurrence [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Procedure occurrence [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Measurement [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 1001: Drug exposure [-365, -1]     ✓ 0 rows returned   Saving _problems/test-executeSpec-integration-475.R   Cohorts created in table main.cohort   Connecting using SQLite driver   ▶ == Executing 3 analysis spec(s) ============================   • Executing spec 1001: Condition occurrence [-365, -1]     ✓ 0 rows returned   • Executing spec 2001: Drug exposure [-365, -1]     ✓ 0 rows returned   • Executing spec 3001: Procedure occurrence [-365, -1]     ✓ 0 rows returned   ✓ Complete: 3 succeeded, 0 failed out of 3   Cohorts created in table main.cohort   Connecting using SQLite driver        |     | | 0%     |     |======================= | 33%     |     |=============================================== | 67%     |     |======================================================================| 100%   Executing SQL took 0.00645 secs   ✓ Created #concept_sets_c with 1 concept set(s): gi   • Executing spec 10301: Concept set: gi (Condition occurrence) [-365, -1]     ✓ 0 rows returned   Cohorts created in table main.cohort   Connecting using SQLite driver   • Executing spec 100101: Cohort: Celecoxib [-365, -1]     ✓ 0 rows returned   Characterization Analysis Plan   ========================================      Analysis Windows: 1   Base Feature Domains: 1 of 9 enabled      condition_occurrence   Cohort Features: disabled   Concept Set Features: disabled   Single Node Analysis Specifications   ========================================   Total specs: 1        base : 1      First 5 analyses:     [1] Condition occurrence [-30, -1] (id=1001)   Single Node Spec   ------------------------------     Analysis ID: 1001     Name: Condition occurrence [-30, -1]     Table: condition_occurrence     Window: [-30, -1]     Type: start     Overlap: FALSE     ATC: FALSE     Concept Set: FALSE     Aggregated: TRUE     Source: base   [ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-covariateData.R:133:3'): .assembleCovariateData produces empty CovariateData when no results ──   Error: not an error   Backtrace:        ▆     1. └─Eunomia::getEunomiaConnectionDetails() at test-covariateData.R:133:3     2. └─Eunomia::getDatabaseFile(...)     3. └─Eunomia::extractLoadData(...)     4. └─Eunomia::loadDataFiles(...)     5. ├─DBI::dbExecute(conn = connection, statement = statement)     6. └─DBI::dbExecute(conn = connection, statement = statement)     7. ├─DBI::dbSendStatement(conn, statement, ...)     8. └─DBI::dbSendStatement(conn, statement, ...)     9. ├─DBI::dbSendQuery(conn, statement, ...)    10. └─RSQLite::dbSendQuery(conn, statement, ...)    11. └─RSQLite (local) .local(conn, statement, ...)    12. ├─methods::new(...)    13. │ ├─methods::initialize(value, ...)    14. │ └─methods::initialize(value, ...)    15. └─RSQLite:::result_create(conn@ptr, statement)   ── Failure ('test-covariateData.R:323:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──   Expected `nrow(covDf) > 0L` to be TRUE.   Differences:   `actual`: FALSE   `expected`: TRUE      ── Failure ('test-covariateData.R:328:3'): getDbOcmCovariateData produces valid CovariateData with Eunomia ──   Expected `nrow(refDf) > 0L` to be TRUE.   Differences:   `actual`: FALSE   `expected`: TRUE      ── Failure ('test-executeSpec-integration.R:475:3'): executeSpec works with drug_exposure domain ──   Expected `nrow(result) > 0` to be TRUE.   Differences:   `actual`: FALSE   `expected`: TRUE         [ FAIL 4 | WARN 0 | SKIP 0 | PASS 535 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [11s/24s] OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR