Last updated on 2026-02-03 19:51:21 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.5 | 8.28 | 653.65 | 661.93 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.5 | 5.97 | 452.37 | 458.34 | OK | |
| 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 | 15.00 | 1073.11 | 1088.11 | ERROR | |
| r-devel-windows-x86_64 | 1.1.5 | 10.00 | 530.00 | 540.00 | OK | |
| r-patched-linux-x86_64 | 1.1.5 | 8.85 | 626.27 | 635.12 | OK | |
| r-release-linux-x86_64 | 1.1.5 | 8.78 | 631.06 | 639.84 | OK | |
| 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 | 14.00 | 764.00 | 778.00 | OK |
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’ [12m/26m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(DrugExposureDiagnostics)
>
> test_check("DrugExposureDiagnostics")
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:37:25.006151
========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:37:27.96307
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:39:26.098357
========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:39:33.124603
population after earliestStartDate smaller than sample, sampling ignored
Saving _problems/test-SummariseChecks-213.R
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:41:09.722975
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:41:14.842285
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:41:28.8094
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:41:33.540888
Progress: getting descendant concepts of ingredient (1125315) used in database
Progress: getting descendant concepts of ingredient
Progress: adding drug strength info
Progress: limiting to concepts in the db
Progress: adding concept names
Overall time taken: 0 minutes and 7 seconds
Time taken: 0 minutes and 8 seconds
Progress: getting drug records for ingredient
Time taken: 0 minutes and 1 seconds
Progress: get concepts used
Time taken: 0 minutes and 1 seconds
Progress: sampling drug records
population after earliestStartDate smaller than sample, sampling ignored
Time taken: 0 minutes and 0 seconds
Progress: check drugsMissing
Time taken: 0 minutes and 7 seconds
Progress: check ExposureDuration
Time taken: 0 minutes and 0 seconds
Progress: check drugQuantity
Time taken: 0 minutes and 0 seconds
Finished
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:45:38.111527
========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:45:45.525219
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:51:05.321796
========>---------------------- 1/4 group-strata combinations @ 2026-02-03 11...
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:51:14.339788
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
Saving _problems/test-executeChecks-373.R
i The following estimates will be calculated:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-03 11:58:31.64937
===============>--------------- 2/4 group-strata combinations @ 2026-02-03 11...
======================>-------- 3/4 group-strata combinations @ 2026-02-03 11...
==============================> 4/4 group-strata combinations @ 2026-02-03 11...
v Summary finished, at 2026-02-03 11:58:35.794727
Time taken: 0 minutes and 0 seconds
testMessage
[ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• Skipping (1): 'test-shiny.R:2:3'
• Sys.getenv("TESTDB_USER2222") == "" is TRUE (1):
'test-SyntheaSqlServer.R:5:3'
• does not work with latest omopgenerics (3): 'test-runBenchmark.R:2:3',
'test-runBenchmark.R:36:3', 'test-runBenchmark.R:47:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SummariseChecks.R:213:3'): summariseChecks partial inputs with combination of not empty and empty ingredient: summary of missing and quantity and dose ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `bind_rows(...)`: Can't combine `..1$dose_form` <character> and `..2$dose_form` <integer>.
Backtrace:
▆
1. ├─DrugExposureDiagnostics::executeChecks(...) at test-SummariseChecks.R:213:3
2. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))
3. │ └─base (local) `<fn>`(f = `<fn>`, `<named list>`, `<named list>`)
4. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
5. │ └─base (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
6. │ └─dplyr (local) rbind(deparse.level, ...)
7. │ └─dplyr::bind_rows(...)
8. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
9. │ └─vctrs (local) `<fn>`()
10. │ └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...)
11. │ └─vctrs:::rww_ptype2(x, y, ...)
12. │ ├─dplyr::rowwise(df_ptype2(x, y, ...))
13. │ └─vctrs::df_ptype2(x, y, ...)
14. └─vctrs (local) `<fn>`()
15. └─vctrs::vec_default_ptype2(...)
16. ├─base::withRestarts(...)
17. │ └─base (local) withOneRestart(expr, restarts[[1L]])
18. │ └─base (local) doWithOneRestart(return(expr), restart)
19. └─vctrs::stop_incompatible_type(...)
20. └─vctrs:::stop_incompatible(...)
21. └─vctrs:::stop_vctrs(...)
22. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-executeChecks.R:370:3'): results from multiple ingredients should be joined also if there is one in between that doesn't exist ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `bind_rows(...)`: Can't combine `..1$dose_form` <character> and `..2$dose_form` <integer>.
Backtrace:
▆
1. ├─DrugExposureDiagnostics (local) executeChecksMock(...) at test-executeChecks.R:370:3
2. │ └─DrugExposureDiagnostics::executeChecks(...) at test-executeChecks.R:14:3
3. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))
4. │ └─base (local) `<fn>`(f = `<fn>`, `<named list>`, `<named list>`, `<named list>`)
5. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
6. │ └─base (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]])
7. │ └─dplyr (local) rbind(deparse.level, ...)
8. │ └─dplyr::bind_rows(...)
9. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
10. │ └─vctrs (local) `<fn>`()
11. │ └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...)
12. │ └─vctrs:::rww_ptype2(x, y, ...)
13. │ ├─dplyr::rowwise(df_ptype2(x, y, ...))
14. │ └─vctrs::df_ptype2(x, y, ...)
15. └─vctrs (local) `<fn>`()
16. └─vctrs::vec_default_ptype2(...)
17. ├─base::withRestarts(...)
18. │ └─base (local) withOneRestart(expr, restarts[[1L]])
19. │ └─base (local) doWithOneRestart(return(expr), restart)
20. └─vctrs::stop_incompatible_type(...)
21. └─vctrs:::stop_incompatible(...)
22. └─vctrs:::stop_vctrs(...)
23. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
[ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc