Last updated on 2026-02-15 01:53:28 CET.
| Package | ERROR | OK |
|---|---|---|
| DrugExposureDiagnostics | 9 | 5 |
| FeatureExtraction | 14 | |
| TestGenerator | 1 | 13 |
Current CRAN status: ERROR: 9, OK: 5
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [433s/591s]
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 2026-02-12 17:16:04.857407
v Summary finished, at 2026-02-12 17:16:06.639488
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 2026-02-12 17:16:54.729917
v Summary finished, at 2026-02-12 17:16:56.62643
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 2026-02-12 17:17:31.086817
v Summary finished, at 2026-02-12 17:17:32.396672
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 2026-02-12 17:17:36.986422
v Summary finished, at 2026-02-12 17:17:38.105155
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 1 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 2026-02-12 17:19:17.551029
v Summary finished, at 2026-02-12 17:19:19.167517
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 2026-02-12 17:21:15.602652
v Summary finished, at 2026-02-12 17:21:16.924456
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 2026-02-12 17:23:51.92977
v Summary finished, at 2026-02-12 17:23:53.749034
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’ [285s/373s]
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 2026-02-14 13:15:57.110025
v Summary finished, at 2026-02-14 13:15:57.920971
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 2026-02-14 13:16:27.116994
v Summary finished, at 2026-02-14 13:16:28.181377
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 2026-02-14 13:16:54.726402
v Summary finished, at 2026-02-14 13:16:55.620454
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 2026-02-14 13:16:59.345425
v Summary finished, at 2026-02-14 13:17:00.646694
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 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 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 2026-02-14 13:18:04.329565
v Summary finished, at 2026-02-14 13:18:05.290141
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 2026-02-14 13:19:10.871035
v Summary finished, at 2026-02-14 13:19:11.846309
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 2026-02-14 13:20:49.401929
v Summary finished, at 2026-02-14 13:20:50.151755
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' [325s]
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 2026-02-14 10:45:22.80485
v Summary finished, at 2026-02-14 10:45:23.563695
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 2026-02-14 10:45:49.598517
v Summary finished, at 2026-02-14 10:45:50.579499
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 2026-02-14 10:46:09.914973
v Summary finished, at 2026-02-14 10:46:10.673179
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 2026-02-14 10:46:13.552452
v Summary finished, at 2026-02-14 10:46:14.450134
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 2026-02-14 10:47:08.06497
v Summary finished, at 2026-02-14 10:47:09.145433
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 2026-02-14 10:48:17.243705
v Summary finished, at 2026-02-14 10:48:17.916126
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 2026-02-14 10:49:38.70991
v Summary finished, at 2026-02-14 10:49:39.720806
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’ [415s/590s]
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 2026-02-14 05:15:31.906965
v Summary finished, at 2026-02-14 05:15:33.765736
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 2026-02-14 05:16:23.448795
===============>--------------- 2/4 group-strata combinations @ 2026-02-14 05...
==============================> 4/4 group-strata combinations @ 2026-02-14 05...
v Summary finished, at 2026-02-14 05:16:25.669906
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 2026-02-14 05:17:01.185622
v Summary finished, at 2026-02-14 05:17:02.28971
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 2026-02-14 05:17:06.013912
v Summary finished, at 2026-02-14 05:17:07.048508
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 2026-02-14 05:18:32.978235
v Summary finished, at 2026-02-14 05:18:35.364121
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 2026-02-14 05:20:39.448844
v Summary finished, at 2026-02-14 05:20:41.014148
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 2026-02-14 05:23:05.79578
v Summary finished, at 2026-02-14 05:23:07.011036
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' [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 2026-02-13 10:32:00.913444
v Summary finished, at 2026-02-13 10:32:01.698567
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 2026-02-13 10:32:27.562461
v Summary finished, at 2026-02-13 10:32:28.676764
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 2026-02-13 10:32:48.001267
v Summary finished, at 2026-02-13 10:32:48.788686
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 2026-02-13 10:32:51.635709
v Summary finished, at 2026-02-13 10:32:52.399199
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 2026-02-13 10:33:48.049742
v Summary finished, at 2026-02-13 10:33:49.162866
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 2026-02-13 10:34:56.382322
v Summary finished, at 2026-02-13 10:34:57.131797
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 2026-02-13 10:36:17.086451
v Summary finished, at 2026-02-13 10:36:17.850351
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-windows-x86_64
Version: 1.1.5
Check: tests
Result: ERROR
Running 'testthat.R' [493s]
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 2026-02-13 12:45:28.972317
v Summary finished, at 2026-02-13 12:45:30.297126
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 2026-02-13 12:46:08.37654
v Summary finished, at 2026-02-13 12:46:09.920126
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 2026-02-13 12:46:37.802972
v Summary finished, at 2026-02-13 12:46:38.985238
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 2026-02-13 12:46:43.202687
v Summary finished, at 2026-02-13 12:46:44.357767
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 2026-02-13 12:48:04.496591
v Summary finished, at 2026-02-13 12:48:06.192874
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 2026-02-13 12:49:42.485824
v Summary finished, at 2026-02-13 12:49:43.586212
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 2026-02-13 12:52:01.426261
v Summary finished, at 2026-02-13 12:52:02.539721
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
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 0.5.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘arrow’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64