Package: CDMConnector
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘a01_getting-started.Rmd’ using rmarkdown
  trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
  Content type 'application/zip' length 6754786 bytes (6.4 MB)
  ==================================================
  downloaded 6.4 MB
  
  Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
  --- finished re-building ‘a01_getting-started.Rmd’
  
  --- re-building ‘a02_cohorts.Rmd’ using rmarkdown
  trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
  Content type 'application/zip' length 6754786 bytes (6.4 MB)
  ==================================================
  downloaded 6.4 MB
  
  --- finished re-building ‘a02_cohorts.Rmd’
  
  --- re-building ‘a03_dbplyr.Rmd’ using rmarkdown
  trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
  Content type 'application/zip' length 6754786 bytes (6.4 MB)
  ==================================================
  downloaded 6.4 MB
  
  --- finished re-building ‘a03_dbplyr.Rmd’
  
  Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
  --- re-building ‘a04_DBI_connection_examples.Rmd’ using rmarkdown
  --- finished re-building ‘a04_DBI_connection_examples.Rmd’
  
  --- re-building ‘a05_cdm_reference_backends.Rmd’ using rmarkdown
  trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
  Content type 'application/zip' length 6754786 bytes (6.4 MB)
  ==================================================
  downloaded 6.4 MB
  
  --- finished re-building ‘a05_cdm_reference_backends.Rmd’
  
  --- re-building ‘a06_using_cdm_attributes.Rmd’ using rmarkdown
  trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
  Content type 'application/zip' length 6754786 bytes (6.4 MB)
  ==================================================
  downloaded 6.4 MB
  
  Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
  
  Quitting from lines 86-96 [unnamed-chunk-9] (a06_using_cdm_attributes.Rmd)
  Error: processing vignette 'a06_using_cdm_attributes.Rmd' failed with diagnostics:
  No known SQL translation
  --- failed re-building ‘a06_using_cdm_attributes.Rmd’
  
  Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
  Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
  SUMMARY: processing the following file failed:
    ‘a06_using_cdm_attributes.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: CDMConnector
Check: tests
New result: ERROR
    Running ‘testthat.R’ [68s/85s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # This file is part of the standard setup for testthat.
    > # It is recommended that you do not modify it.
    > #
    > # Where should you do additional test configuration?
    > # Learn more about the roles of various files in:
    > # * https://r-pkgs.org/tests.html
    > # * https://testthat.r-lib.org/reference/test_package.html#special-files
    > 
    > library(testthat)
    > library(CDMConnector)
    > 
    > test_check("CDMConnector")
    trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
    Content type 'application/zip' length 6754786 bytes (6.4 MB)
    ==================================================
    downloaded 6.4 MB
    
    
    Download completed!
    Creating CDM database /home/hornik/tmp/scratch/RtmpTAhcjP/file358ee7707a3134/GiBleed_5.3.zip
    [ FAIL 5 | WARN 0 | SKIP 18 | PASS 196 ]
    
    ══ Skipped tests (18) ══════════════════════════════════════════════════════════
    • Capr cannot be loaded (1): 'test-db-generateCohortSet.R:77:3'
    • CirceR cannot be loaded (8): 'test-db-custom_cohort_creation.R:42:5',
      'test-db-generateCohortSet.R:64:5', 'test-db-generateCohortSet.R:210:3',
      'test-db-generateConceptCohortSet.R:282:5',
      'test-db-newGeneratedCohortSet.R:126:3',
      'test-db-newGeneratedCohortSet.R:179:3',
      'test-db-recordCohortAttrition.R:133:3',
      'test-write_prefix_cohort_generation_snowflake.R:3:3'
    • TreatmentPatterns cannot be loaded (1): 'test-db-generateCohortSet.R:127:3'
    • arrow cannot be loaded (1): 'test-local_cdm.R:3:3'
    • eunomia_is_available("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
    • failing test (1): 'test-db-dateadd.R:126:3'
    • manual test (5): 'test-Eunomia.R:2:3', 'test-db-copy_cdm_to.R:62:3',
      'test-db-generateCohortSet.R:108:3', 'test-db-generateCohortSet.R:243:3',
      'test-db-write_schema_with_database.R:5:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-db-cohortTransformations.R:258:5'): duckdb - cohort_collapse ───
    Error in `dbplyr::win_over()`: No known SQL translation
    Backtrace:
         ▆
      1. ├─CDMConnector (local) test_cohort_collapse(con, write_schema) at test-db-cohortTransformations.R:258:5
      2. │ └─... %>% ... at test-db-cohortTransformations.R:74:3
      3. ├─dplyr::mutate(., dplyr::across(dplyr::matches("id"), as.double))
      4. ├─dplyr::mutate(., dplyr::across(dplyr::matches("date"), as.Date))
      5. ├─dplyr::arrange(...)
      6. ├─dplyr::tibble(.)
      7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
      8. │   └─rlang::eval_tidy(xs[[j]], mask)
      9. ├─dplyr::collect(.)
     10. ├─dbplyr:::collect.tbl_sql(.)
     11. │ └─dbplyr::db_sql_render(x$src$con, x, cte = cte)
     12. │   ├─dbplyr::db_sql_render(con, sql, ..., sql_options = sql_options)
     13. │   └─dbplyr:::db_sql_render.DBIConnection(con, sql, ..., sql_options = sql_options)
     14. │     ├─dbplyr::sql_render(sql, con = con, ..., sql_options = sql_options)
     15. │     └─dbplyr:::sql_render.tbl_lazy(sql, con = con, ..., sql_options = sql_options)
     16. │       ├─dbplyr::sql_render(...)
     17. │       └─dbplyr:::sql_render.lazy_query(...)
     18. │         ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
     19. │         └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
     20. │           ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     21. │           └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     22. │             ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     23. │             └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     24. │               └─dbplyr:::get_select_sql(...)
     25. │                 └─dbplyr:::translate_select_sql(con, select)
     26. │                   └─dbplyr::translate_sql_(...)
     27. │                     └─base::lapply(...)
     28. │                       └─dbplyr (local) FUN(X[[i]], ...)
     29. │                         ├─dbplyr::escape(eval_tidy(x, mask), con = con)
     30. │                         └─rlang::eval_tidy(x, mask)
     31. ├─dplyr::coalesce(...)
     32. └─dbplyr::win_over
     33.   └─cli::cli_abort(...)
     34.     └─rlang::abort(...)
    ── Failure ('test-db-generateConceptCohortSet.R:322:5'): Regimen domain does not cause error ──
    Expected `{ ... }` to run without any errors.
    i Actually got a <rlang_error> with text:
      No known SQL translation
    ── Failure ('test-db-generateConceptCohortSet.R:328:3'): Regimen domain does not cause error ──
    cdm$cohort is not an S3 object
    ── Error ('test-db-recordCohortAttrition.R:127:5'): duckdb - recordCohortAttrition ──
    Error in `dbplyr::win_over()`: No known SQL translation
    Backtrace:
         ▆
      1. ├─CDMConnector (local) test_record_cohort_attrition(con, cdm_schema, write_schema) at test-db-recordCohortAttrition.R:127:5
      2. │ └─CDMConnector::generateConceptCohortSet(...) at test-db-recordCohortAttrition.R:9:3
      3. │   └─... %>% ...
      4. ├─dplyr::compute(., name = name, temporary = FALSE, overwrite = overwrite)
      5. ├─omopgenerics:::compute.cdm_table(...)
      6. │ ├─dplyr::compute(...)
      7. │ └─CDMConnector:::compute.db_cdm(...)
      8. │   └─CDMConnector:::.computeQuery(...)
      9. │     └─dbplyr::sql_render(x)
     10. │       ├─dbplyr::sql_render(...)
     11. │       └─dbplyr:::sql_render.tbl_lazy(...)
     12. │         ├─dbplyr::sql_render(...)
     13. │         └─dbplyr:::sql_render.lazy_query(...)
     14. │           ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
     15. │           └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
     16. │             ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     17. │             └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     18. │               ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     19. │               └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     20. │                 ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     21. │                 └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     22. │                   └─dbplyr:::get_select_sql(...)
     23. │                     └─dbplyr:::translate_select_sql(con, select)
     24. │                       └─dbplyr::translate_sql_(...)
     25. │                         └─base::lapply(...)
     26. │                           └─dbplyr (local) FUN(X[[i]], ...)
     27. │                             ├─dbplyr::escape(eval_tidy(x, mask), con = con)
     28. │                             └─rlang::eval_tidy(x, mask)
     29. ├─dplyr::coalesce(...)
     30. └─dbplyr::win_over
     31.   └─cli::cli_abort(...)
     32.     └─rlang::abort(...)
    ── Error ('test-memory-issue.R:14:3'): memory leak does not happen ─────────────
    Error in `dbplyr::win_over()`: No known SQL translation
    Backtrace:
         ▆
      1. ├─CDMConnector::generateConceptCohortSet(...) at test-memory-issue.R:14:3
      2. │ └─... %>% ...
      3. ├─dplyr::compute(., name = name, temporary = FALSE, overwrite = overwrite)
      4. ├─omopgenerics:::compute.cdm_table(...)
      5. │ ├─dplyr::compute(...)
      6. │ └─CDMConnector:::compute.db_cdm(...)
      7. │   └─CDMConnector:::.computeQuery(...)
      8. │     └─dbplyr::sql_render(x)
      9. │       ├─dbplyr::sql_render(...)
     10. │       └─dbplyr:::sql_render.tbl_lazy(...)
     11. │         ├─dbplyr::sql_render(...)
     12. │         └─dbplyr:::sql_render.lazy_query(...)
     13. │           ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
     14. │           └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
     15. │             ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     16. │             └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     17. │               ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     18. │               └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     19. │                 ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
     20. │                 └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
     21. │                   └─dbplyr:::get_select_sql(...)
     22. │                     └─dbplyr:::translate_select_sql(con, select)
     23. │                       └─dbplyr::translate_sql_(...)
     24. │                         └─base::lapply(...)
     25. │                           └─dbplyr (local) FUN(X[[i]], ...)
     26. │                             ├─dbplyr::escape(eval_tidy(x, mask), con = con)
     27. │                             └─rlang::eval_tidy(x, mask)
     28. ├─dplyr::coalesce(...)
     29. └─dbplyr::win_over
     30.   └─cli::cli_abort(...)
     31.     └─rlang::abort(...)
    
    [ FAIL 5 | WARN 0 | SKIP 18 | PASS 196 ]
    Error: Test failures
    In addition: Warning messages:
    1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
    2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
    3: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
    4: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
    5: Connection is garbage-collected, use dbDisconnect() to avoid this. 
    6: Connection is garbage-collected, use dbDisconnect() to avoid this. 
    Execution halted
    Warning messages:
    1: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
    2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.