Running ‘testthat.R’ [12m/26m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DrugExposureDiagnostics)
  > 
  > test_check("DrugExposureDiagnostics")
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  population after earliestStartDate smaller than sample, sampling ignored
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:37:25.006151
  ========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
  ======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:37:27.96307
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:39:26.098357
  ========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
  ======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:39:33.124603
  population after earliestStartDate smaller than sample, sampling ignored
  Saving _problems/test-SummariseChecks-213.R
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:41:09.722975
  ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
  ======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:41:14.842285
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:41:28.8094
  ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:41:33.540888
  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 7 seconds
  Time taken: 0 minutes and 8 seconds
  Progress: getting drug records for ingredient
  Time taken: 0 minutes and 1 seconds
  Progress: get concepts used
  Time taken: 0 minutes and 1 seconds
  Progress: sampling drug records
  population after earliestStartDate smaller than sample, sampling ignored
  Time taken: 0 minutes and 0 seconds
  Progress: check drugsMissing
  Time taken: 0 minutes and 7 seconds
  Progress: check ExposureDuration
  Time taken: 0 minutes and 0 seconds
  Progress: check drugQuantity
  Time taken: 0 minutes and 0 seconds
  Finished
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:45:38.111527
  ========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
  ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
  ======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:45:45.525219
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:51:05.321796
  ========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
  ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
  ======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:51:14.339788
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  population after earliestStartDate smaller than sample, sampling ignored
  Saving _problems/test-executeChecks-373.R
  i The following estimates will be calculated:
  * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-03 11:58:31.64937
  ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
  ======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
  ==============================> 4/4 group-strata combinations @ 2026-02-03 11...
  v Summary finished, at 2026-02-03 11:58:35.794727
  Time taken: 0 minutes and 0 seconds
  testMessage
  [ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • Skipping (1): 'test-shiny.R:2:3'
  • Sys.getenv("TESTDB_USER2222") == "" is TRUE (1):
    'test-SyntheaSqlServer.R:5:3'
  • does not work with latest omopgenerics (3): 'test-runBenchmark.R:2:3',
    'test-runBenchmark.R:36:3', 'test-runBenchmark.R:47:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-SummariseChecks.R:213:3'): summariseChecks partial inputs with combination of not empty and empty ingredient: summary of missing and quantity and dose ──
  <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
  Error in `bind_rows(...)`: Can't combine `..1$dose_form` <character> and `..2$dose_form` <integer>.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics::executeChecks(...) at test-SummariseChecks.R:213:3
    2. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))
    3. │ └─base (local) `<fn>`(f = `<fn>`, `<named list>`, `<named list>`)
    4. │   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
    5. │     └─base (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
    6. │       └─dplyr (local) rbind(deparse.level, ...)
    7. │         └─dplyr::bind_rows(...)
    8. │           └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
    9. │             └─vctrs (local) `<fn>`()
   10. │               └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...)
   11. │                 └─vctrs:::rww_ptype2(x, y, ...)
   12. │                   ├─dplyr::rowwise(df_ptype2(x, y, ...))
   13. │                   └─vctrs::df_ptype2(x, y, ...)
   14. └─vctrs (local) `<fn>`()
   15.   └─vctrs::vec_default_ptype2(...)
   16.     ├─base::withRestarts(...)
   17.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
   18.     │   └─base (local) doWithOneRestart(return(expr), restart)
   19.     └─vctrs::stop_incompatible_type(...)
   20.       └─vctrs:::stop_incompatible(...)
   21.         └─vctrs:::stop_vctrs(...)
   22.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  ── Error ('test-executeChecks.R:370:3'): results from multiple ingredients should be joined also if there is one in between that doesn't exist ──
  <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
  Error in `bind_rows(...)`: Can't combine `..1$dose_form` <character> and `..2$dose_form` <integer>.
  Backtrace:
       ▆
    1. ├─DrugExposureDiagnostics (local) executeChecksMock(...) at test-executeChecks.R:370:3
    2. │ └─DrugExposureDiagnostics::executeChecks(...) at test-executeChecks.R:14:3
    3. │   ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))
    4. │   └─base (local) `<fn>`(f = `<fn>`, `<named list>`, `<named list>`, `<named list>`)
    5. │     └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
    6. │       └─base (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]])
    7. │         └─dplyr (local) rbind(deparse.level, ...)
    8. │           └─dplyr::bind_rows(...)
    9. │             └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
   10. │               └─vctrs (local) `<fn>`()
   11. │                 └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...)
   12. │                   └─vctrs:::rww_ptype2(x, y, ...)
   13. │                     ├─dplyr::rowwise(df_ptype2(x, y, ...))
   14. │                     └─vctrs::df_ptype2(x, y, ...)
   15. └─vctrs (local) `<fn>`()
   16.   └─vctrs::vec_default_ptype2(...)
   17.     ├─base::withRestarts(...)
   18.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
   19.     │   └─base (local) doWithOneRestart(return(expr), restart)
   20.     └─vctrs::stop_incompatible_type(...)
   21.       └─vctrs:::stop_incompatible(...)
   22.         └─vctrs:::stop_vctrs(...)
   23.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  
  [ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ]
  Error:
  ! Test failures.
  Execution halted