Running ‘testthat.R’ [73s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DrugExposureDiagnostics)
  > 
  > test_check("DrugExposureDiagnostics")
  trying URL 'https://raw.githubusercontent.com/darwin-eu/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
  Content type 'application/zip' length 6848518 bytes (6.5 MB)
  ==================================================
  downloaded 6.5 MB
  
  attempting to extract and load /home/hornik/tmp/scratch/RtmpYs7SmW/GiBleed_5.3.zip
  Progress: getting descendant concepts of ingredient (1125315) used in database
  Progress: getting descendant concepts of ingredient
  Progress: adding drug strength info
  Progress: limiting to concepts in the db
  Progress: adding concept names
  Overall time taken: 0 minutes and 2 seconds
  Time taken: 0 minutes and 2 seconds
  Progress: getting drug strength for ingredient
  Time taken: 0 minutes and 0 seconds
  Progress: getting drug records for ingredient
  Time taken: 0 minutes and 0 seconds
  Progress: get concepts used
  Time taken: 0 minutes and 0 seconds
  Progress: get ingredient overview
  Time taken: 0 minutes and 0 seconds
  testMessage
  [ FAIL 10 | WARN 0 | SKIP 1 | PASS 176 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Sys.getenv("TESTDB_USER") == "" is TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Eunomia.R:5'): execute all checks, default ingredient, verbose ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics::executeChecks(cdm, verbose = TRUE) at test-Eunomia.R:5:2
    2. │ └─DrugExposureDiagnostics:::executeChecksSingleIngredient(...)
    3. │   ├─... %>% dplyr::collect()
    4. │   └─DrugExposureDiagnostics:::getIngredientOverview(...)
    5. │     ├─... %>% ...
    6. │     └─DrugExposureDiagnostics:::getDuration(...)
    7. │       └─cdm[[tableName]] %>% ...
    8. ├─dplyr::collect(.)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::left_join(...)
   11. ├─dplyr::mutate(...)
   12. ├─dbplyr:::mutate.tbl_lazy(...)
   13. │ └─dbplyr:::get_mutate_layers(.data, ...)
   14. │   ├─base::as.list(enquos(..., .named = TRUE))
   15. │   └─rlang::enquos(..., .named = TRUE)
   16. │     └─rlang:::endots(...)
   17. │       └─rlang:::map(...)
   18. │         └─base::lapply(.x, .f, ...)
   19. │           └─rlang (local) FUN(X[[i]], ...)
   20. │             └─rlang::splice(...)
   21. └─CDMConnector::datediff(...)
   22.   └─rlang::check_installed("SqlRender")
  ── Error ('test-Eunomia.R:25'): execute all checks, given ingredient ───────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics::executeChecks(cdm, 1125315) at test-Eunomia.R:25:2
    2. │ └─DrugExposureDiagnostics:::executeChecksSingleIngredient(...)
    3. │   ├─... %>% dplyr::collect()
    4. │   └─DrugExposureDiagnostics:::getIngredientOverview(...)
    5. │     ├─... %>% ...
    6. │     └─DrugExposureDiagnostics:::getDuration(...)
    7. │       └─cdm[[tableName]] %>% ...
    8. ├─dplyr::collect(.)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::left_join(...)
   11. ├─dplyr::mutate(...)
   12. ├─dbplyr:::mutate.tbl_lazy(...)
   13. │ └─dbplyr:::get_mutate_layers(.data, ...)
   14. │   ├─base::as.list(enquos(..., .named = TRUE))
   15. │   └─rlang::enquos(..., .named = TRUE)
   16. │     └─rlang:::endots(...)
   17. │       └─rlang:::map(...)
   18. │         └─base::lapply(.x, .f, ...)
   19. │           └─rlang (local) FUN(X[[i]], ...)
   20. │             └─rlang::splice(...)
   21. └─CDMConnector::datediff(...)
   22.   └─rlang::check_installed("SqlRender")
  ── Error ('test-Eunomia.R:38'): execute some checks, given ingredient ──────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics::executeChecks(...) at test-Eunomia.R:38:2
    2. │ └─DrugExposureDiagnostics:::executeChecksSingleIngredient(...)
    3. │   ├─... %>% dplyr::collect()
    4. │   └─DrugExposureDiagnostics:::getIngredientOverview(...)
    5. │     ├─... %>% ...
    6. │     └─DrugExposureDiagnostics:::getDuration(...)
    7. │       └─cdm[[tableName]] %>% ...
    8. ├─dplyr::collect(.)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::left_join(...)
   11. ├─dplyr::mutate(...)
   12. ├─dbplyr:::mutate.tbl_lazy(...)
   13. │ └─dbplyr:::get_mutate_layers(.data, ...)
   14. │   ├─base::as.list(enquos(..., .named = TRUE))
   15. │   └─rlang::enquos(..., .named = TRUE)
   16. │     └─rlang:::endots(...)
   17. │       └─rlang:::map(...)
   18. │         └─base::lapply(.x, .f, ...)
   19. │           └─rlang (local) FUN(X[[i]], ...)
   20. │             └─rlang::splice(...)
   21. └─CDMConnector::datediff(...)
   22.   └─rlang::check_installed("SqlRender")
  ── Error ('test-Eunomia.R:132'): get number of Days_supply that are incorrect ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = "drug_exposure_start_date", end = "drug_exposure_end_date", 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics:::checkDaysSupply(cdm, drugRecordsTable = "ingredient_drug_records") at test-Eunomia.R:132:2
    2. │ └─... %>% dplyr::collect()
    3. ├─dplyr::collect(.)
    4. ├─dplyr::mutate(...)
    5. ├─dbplyr:::mutate.tbl_lazy(...)
    6. │ └─dbplyr:::get_mutate_layers(.data, ...)
    7. │   ├─base::as.list(enquos(..., .named = TRUE))
    8. │   └─rlang::enquos(..., .named = TRUE)
    9. │     └─rlang:::endots(...)
   10. │       └─rlang:::map(...)
   11. │         └─base::lapply(.x, .f, ...)
   12. │           └─rlang (local) FUN(X[[i]], ...)
   13. │             └─rlang::splice(...)
   14. └─CDMConnector::datediff(...)
   15.   └─rlang::check_installed("SqlRender")
  ── Error ('test-Eunomia.R:145'): sampling ──────────────────────────────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics::executeChecks(...) at test-Eunomia.R:145:2
    2. │ └─DrugExposureDiagnostics:::executeChecksSingleIngredient(...)
    3. │   ├─... %>% dplyr::collect()
    4. │   └─DrugExposureDiagnostics:::getIngredientOverview(...)
    5. │     ├─... %>% ...
    6. │     └─DrugExposureDiagnostics:::getDuration(...)
    7. │       └─cdm[[tableName]] %>% ...
    8. ├─dplyr::collect(.)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::left_join(...)
   11. ├─dplyr::mutate(...)
   12. ├─dbplyr:::mutate.tbl_lazy(...)
   13. │ └─dbplyr:::get_mutate_layers(.data, ...)
   14. │   ├─base::as.list(enquos(..., .named = TRUE))
   15. │   └─rlang::enquos(..., .named = TRUE)
   16. │     └─rlang:::endots(...)
   17. │       └─rlang:::map(...)
   18. │         └─base::lapply(.x, .f, ...)
   19. │           └─rlang (local) FUN(X[[i]], ...)
   20. │             └─rlang::splice(...)
   21. └─CDMConnector::datediff(...)
   22.   └─rlang::check_installed("SqlRender")
  ── Error ('test-Eunomia.R:165'): summary ───────────────────────────────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics::executeChecks(cdm = cdm, ingredients = 1125315) at test-Eunomia.R:165:2
    2. │ └─DrugExposureDiagnostics:::executeChecksSingleIngredient(...)
    3. │   ├─... %>% dplyr::collect()
    4. │   └─DrugExposureDiagnostics:::getIngredientOverview(...)
    5. │     ├─... %>% ...
    6. │     └─DrugExposureDiagnostics:::getDuration(...)
    7. │       └─cdm[[tableName]] %>% ...
    8. ├─dplyr::collect(.)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::left_join(...)
   11. ├─dplyr::mutate(...)
   12. ├─dbplyr:::mutate.tbl_lazy(...)
   13. │ └─dbplyr:::get_mutate_layers(.data, ...)
   14. │   ├─base::as.list(enquos(..., .named = TRUE))
   15. │   └─rlang::enquos(..., .named = TRUE)
   16. │     └─rlang:::endots(...)
   17. │       └─rlang:::map(...)
   18. │         └─base::lapply(.x, .f, ...)
   19. │           └─rlang (local) FUN(X[[i]], ...)
   20. │             └─rlang::splice(...)
   21. └─CDMConnector::datediff(...)
   22.   └─rlang::check_installed("SqlRender")
  ── Error ('test-IngredientOverview.R:35'): getIngredientOverview ───────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─... %>% dplyr::collect() at test-IngredientOverview.R:35:2
    2. ├─dplyr::collect(.)
    3. ├─DrugExposureDiagnostics:::getIngredientOverview(...)
    4. │ ├─... %>% ...
    5. │ └─DrugExposureDiagnostics:::getDuration(...)
    6. │   └─cdm[[tableName]] %>% ...
    7. ├─dplyr::mutate(...)
    8. ├─dplyr::left_join(...)
    9. ├─dplyr::mutate(...)
   10. ├─dbplyr:::mutate.tbl_lazy(...)
   11. │ └─dbplyr:::get_mutate_layers(.data, ...)
   12. │   ├─base::as.list(enquos(..., .named = TRUE))
   13. │   └─rlang::enquos(..., .named = TRUE)
   14. │     └─rlang:::endots(...)
   15. │       └─rlang:::map(...)
   16. │         └─base::lapply(.x, .f, ...)
   17. │           └─rlang (local) FUN(X[[i]], ...)
   18. │             └─rlang::splice(...)
   19. └─CDMConnector::datediff(...)
   20.   └─rlang::check_installed("SqlRender")
  ── Error ('test-IngredientOverview.R:64'): getIngredientsPresence ──────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = "drug_exposure_start_date", end = "drug_exposure_end_date", 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─... %>% dplyr::collect() at test-IngredientOverview.R:64:2
    2. ├─dplyr::collect(.)
    3. ├─DrugExposureDiagnostics:::getIngredientPresence(...)
    4. │ └─... %>% ...
    5. ├─dplyr::mutate(...)
    6. ├─dplyr::mutate(...)
    7. ├─dplyr::mutate(...)
    8. ├─dplyr::mutate(...)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::mutate(...)
   11. ├─dplyr::mutate(...)
   12. ├─dplyr::mutate(...)
   13. ├─dbplyr:::mutate.tbl_lazy(...)
   14. │ └─dbplyr:::get_mutate_layers(.data, ...)
   15. │   ├─base::as.list(enquos(..., .named = TRUE))
   16. │   └─rlang::enquos(..., .named = TRUE)
   17. │     └─rlang:::endots(...)
   18. │       └─rlang:::map(...)
   19. │         └─base::lapply(.x, .f, ...)
   20. │           └─rlang (local) FUN(X[[i]], ...)
   21. │             └─rlang::splice(...)
   22. └─CDMConnector::datediff(...)
   23.   └─rlang::check_installed("SqlRender")
  ── Error ('test-checkDaysSupply.R:25'): check if it can detect missing ─────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = "drug_exposure_start_date", end = "drug_exposure_end_date", 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics:::checkDaysSupply(testData, byConcept = TRUE) at test-checkDaysSupply.R:25:2
    2. │ └─... %>% dplyr::collect()
    3. ├─dplyr::collect(.)
    4. ├─dplyr::mutate(...)
    5. ├─dbplyr:::mutate.tbl_lazy(...)
    6. │ └─dbplyr:::get_mutate_layers(.data, ...)
    7. │   ├─base::as.list(enquos(..., .named = TRUE))
    8. │   └─rlang::enquos(..., .named = TRUE)
    9. │     └─rlang:::endots(...)
   10. │       └─rlang:::map(...)
   11. │         └─base::lapply(.x, .f, ...)
   12. │           └─rlang (local) FUN(X[[i]], ...)
   13. │             └─rlang::splice(...)
   14. └─CDMConnector::datediff(...)
   15.   └─rlang::check_installed("SqlRender")
  ── Error ('test-getHistogram.R:27'): test histogram plotting ───────────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::datediff(start = startDateCol, end = endDateCol, 
      interval = "day")`: The package `SqlRender` is required.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics:::createHistogram(...) at test-getHistogram.R:27:2
    2. │ └─DrugExposureDiagnostics:::getDuration(cdm, drugRecordsTable)
    3. │   └─cdm[[tableName]] %>% ...
    4. ├─dplyr::mutate(...)
    5. ├─dbplyr:::mutate.tbl_lazy(...)
    6. │ └─dbplyr:::get_mutate_layers(.data, ...)
    7. │   ├─base::as.list(enquos(..., .named = TRUE))
    8. │   └─rlang::enquos(..., .named = TRUE)
    9. │     └─rlang:::endots(...)
   10. │       └─rlang:::map(...)
   11. │         └─base::lapply(.x, .f, ...)
   12. │           └─rlang (local) FUN(X[[i]], ...)
   13. │             └─rlang::splice(...)
   14. └─CDMConnector::datediff(...)
   15.   └─rlang::check_installed("SqlRender")
  
  [ FAIL 10 | WARN 0 | SKIP 1 | PASS 176 ]
  Error: Test failures
  In addition: There were 36 warnings (use warnings() to see them)
  Execution halted
  There were 12 warnings (use warnings() to see them)