Last updated on 2026-02-12 09:49:38 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.5 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 1.1.5 | 5.56 | 454.94 | 460.50 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.5 | 15.00 | 1058.86 | 1073.86 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.5 | 14.00 | 1042.78 | 1056.78 | ERROR | |
| r-devel-macos-arm64 | 1.1.5 | 2.00 | 136.00 | 138.00 | OK | |
| r-devel-windows-x86_64 | 1.1.5 | 11.00 | 538.00 | 549.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1.5 | 10.09 | 630.46 | 640.55 | ERROR | |
| r-release-linux-x86_64 | 1.1.5 | 7.46 | 625.15 | 632.61 | ERROR | |
| r-release-macos-arm64 | 1.1.5 | OK | ||||
| r-release-macos-x86_64 | 1.1.5 | 5.00 | 427.00 | 432.00 | OK | |
| r-release-windows-x86_64 | 1.1.5 | 10.00 | 528.00 | 538.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.5 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.5 | 5.00 | 383.00 | 388.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.5 | 13.00 | 808.00 | 821.00 | ERROR |
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [436s/593s]
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 2026-02-09 17:15:14.185271
v Summary finished, at 2026-02-09 17:15:15.515521
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 2026-02-09 17:16:03.779497
v Summary finished, at 2026-02-09 17:16:05.515682
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 2026-02-09 17:16:40.038465
v Summary finished, at 2026-02-09 17:16:41.395611
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 2026-02-09 17:16:45.578926
v Summary finished, at 2026-02-09 17:16:46.970789
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 records for ingredient
Time taken: 0 minutes and 0 seconds
Progress: get concepts used
Time taken: 0 minutes and 0 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 3 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 2026-02-09 17:18:26.277105
===============>--------------- 2/4 group-strata combinations @ 2026-02-09 17...
==============================> 4/4 group-strata combinations @ 2026-02-09 17...
v Summary finished, at 2026-02-09 17:18:28.356002
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 2026-02-09 17:20:28.922109
v Summary finished, at 2026-02-09 17:20:30.753314
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 2026-02-09 17:22:56.980726
v Summary finished, at 2026-02-09 17:22:58.456441
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [299s/372s]
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 2026-02-11 13:17:29.305652
v Summary finished, at 2026-02-11 13:17:30.155885
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 2026-02-11 13:18:00.681225
v Summary finished, at 2026-02-11 13:18:02.321161
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 2026-02-11 13:18:23.625949
v Summary finished, at 2026-02-11 13:18:24.402029
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 2026-02-11 13:18:28.265831
v Summary finished, at 2026-02-11 13:18:29.208791
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 1 seconds
Time taken: 0 minutes and 1 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: 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 1 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 2026-02-11 13:19:25.74915
v Summary finished, at 2026-02-11 13:19:26.770924
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 2026-02-11 13:20:39.074675
v Summary finished, at 2026-02-11 13:20:39.96944
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 2026-02-11 13:22:19.321238
v Summary finished, at 2026-02-11 13:22:20.198557
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [12m/16m]
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 12:40:40.217778
v Summary finished, at 2026-02-03 12:40:42.318233
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 12:42:35.772393
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...
==============================> 4/4 group-strata combinations @ 2026-02-03 12...
v Summary finished, at 2026-02-03 12:42:39.883098
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 12:43:38.913646
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...
==============================> 4/4 group-strata combinations @ 2026-02-03 12...
v Summary finished, at 2026-02-03 12:43:41.32061
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 12:43:49.715222
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...
==============================> 4/4 group-strata combinations @ 2026-02-03 12...
v Summary finished, at 2026-02-03 12:43:52.385411
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 3 seconds
Time taken: 0 minutes and 3 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: 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 4 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 12:46:13.210137
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...
==============================> 4/4 group-strata combinations @ 2026-02-03 12...
v Summary finished, at 2026-02-03 12:46:15.91536
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 12:49:13.89034
v Summary finished, at 2026-02-03 12:49:15.686697
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 12:52:31.182264
v Summary finished, at 2026-02-03 12:52:32.96847
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [11m/15m]
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 2026-02-08 00:51:47.01807
v Summary finished, at 2026-02-08 00:51:48.97137
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 2026-02-08 00:53:01.228097
===============>--------------- 2/4 group-strata combinations @ 2026-02-08 00...
======================>-------- 3/4 group-strata combinations @ 2026-02-08 00...
==============================> 4/4 group-strata combinations @ 2026-02-08 00...
v Summary finished, at 2026-02-08 00:53:04.17293
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 2026-02-08 00:53:55.99579
v Summary finished, at 2026-02-08 00:53:58.1483
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 2026-02-08 00:54:05.63718
v Summary finished, at 2026-02-08 00:54:08.037198
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 3 seconds
Time taken: 0 minutes and 4 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: 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 4 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 2026-02-08 00:56:35.828234
===============>--------------- 2/4 group-strata combinations @ 2026-02-08 00...
==============================> 4/4 group-strata combinations @ 2026-02-08 00...
v Summary finished, at 2026-02-08 00:56:39.490019
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 2026-02-08 00:59:55.720297
===============>--------------- 2/4 group-strata combinations @ 2026-02-08 00...
==============================> 4/4 group-strata combinations @ 2026-02-08 00...
v Summary finished, at 2026-02-08 00:59:57.990902
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 2026-02-08 01:03:43.27963
v Summary finished, at 2026-02-08 01:03:45.09191
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.5
Check: tests
Result: ERROR
Running 'testthat.R' [327s]
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 2026-02-05 08:18:04.922931
v Summary finished, at 2026-02-05 08:18:05.711034
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 2026-02-05 08:18:31.991581
v Summary finished, at 2026-02-05 08:18:33.202252
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 2026-02-05 08:18:51.860642
v Summary finished, at 2026-02-05 08:18:52.686158
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 2026-02-05 08:18:55.573276
v Summary finished, at 2026-02-05 08:18:56.448958
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 1 seconds
Time taken: 0 minutes and 1 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: 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 2 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 2026-02-05 08:19:50.211538
v Summary finished, at 2026-02-05 08:19:51.34841
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 2026-02-05 08:20:59.266754
v Summary finished, at 2026-02-05 08:21:00.054264
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 2026-02-05 08:22:21.083775
v Summary finished, at 2026-02-05 08:22:21.903539
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
Flavor: r-devel-windows-x86_64
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [415s/567s]
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 2026-02-11 05:21:40.073852
v Summary finished, at 2026-02-11 05:21:41.483268
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 2026-02-11 05:22:25.2819
v Summary finished, at 2026-02-11 05:22:26.986028
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 2026-02-11 05:22:56.629976
v Summary finished, at 2026-02-11 05:22:57.965058
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 2026-02-11 05:23:02.265972
v Summary finished, at 2026-02-11 05:23:03.298838
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 records for ingredient
Time taken: 0 minutes and 0 seconds
Progress: get concepts used
Time taken: 0 minutes and 0 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 3 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 2026-02-11 05:24:41.985421
===============>--------------- 2/4 group-strata combinations @ 2026-02-11 05...
==============================> 4/4 group-strata combinations @ 2026-02-11 05...
v Summary finished, at 2026-02-11 05:24:44.333913
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 2026-02-11 05:26:41.910784
===============>--------------- 2/4 group-strata combinations @ 2026-02-11 05...
==============================> 4/4 group-strata combinations @ 2026-02-11 05...
v Summary finished, at 2026-02-11 05:26:44.031513
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 2026-02-11 05:29:06.773806
v Summary finished, at 2026-02-11 05:29:08.051434
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
Flavor: r-patched-linux-x86_64
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [412s/531s]
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 2026-02-07 05:12:54.598197
v Summary finished, at 2026-02-07 05:12:55.62463
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 2026-02-07 05:13:32.969832
v Summary finished, at 2026-02-07 05:13:34.557856
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 2026-02-07 05:13:59.983901
v Summary finished, at 2026-02-07 05:14:01.045847
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 2026-02-07 05:14:04.53903
v Summary finished, at 2026-02-07 05:14:05.621517
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 records for ingredient
Time taken: 0 minutes and 0 seconds
Progress: get concepts used
Time taken: 0 minutes and 0 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 2 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 2026-02-07 05:15:29.059407
v Summary finished, at 2026-02-07 05:15:30.670434
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 2026-02-07 05:17:25.181332
v Summary finished, at 2026-02-07 05:17:26.608533
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 2026-02-07 05:19:55.880356
v Summary finished, at 2026-02-07 05:19:57.504708
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
Flavor: r-release-linux-x86_64
Version: 1.1.5
Check: tests
Result: ERROR
Running 'testthat.R' [521s]
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 2026-02-04 08:13:29.334845
v Summary finished, at 2026-02-04 08:13:30.616827
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 2026-02-04 08:14:10.161403
v Summary finished, at 2026-02-04 08:14:11.812082
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 2026-02-04 08:14:39.949232
v Summary finished, at 2026-02-04 08:14:41.154821
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 2026-02-04 08:14:45.65423
v Summary finished, at 2026-02-04 08:14:46.862695
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 records for ingredient
Time taken: 0 minutes and 0 seconds
Progress: get concepts used
Time taken: 0 minutes and 0 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 3 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 2026-02-04 08:16:08.749033
v Summary finished, at 2026-02-04 08:16:10.445087
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 2026-02-04 08:17:52.318109
v Summary finished, at 2026-02-04 08:17:53.721514
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 2026-02-04 08:20:14.77151
v Summary finished, at 2026-02-04 08:20:15.981014
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
Flavor: r-oldrel-windows-x86_64