Last updated on 2026-02-19 11:54:18 CET.
| Package | ERROR | OK |
|---|---|---|
| DrugExposureDiagnostics | 1 | 13 |
| FeatureExtraction | 14 | |
| TestGenerator | 1 | 13 |
Current CRAN status: ERROR: 1, OK: 13
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
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