Last updated on 2024-11-23 07:50:19 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.1 | 6.62 | 1254.18 | 1260.80 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.8.1 | 5.60 | 852.19 | 857.79 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.8.1 | 2076.48 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.8.1 | 1936.42 | ERROR | |||
| r-devel-windows-x86_64 | 0.8.1 | 8.00 | 732.00 | 740.00 | OK | |
| r-patched-linux-x86_64 | 0.8.1 | 6.72 | 1200.09 | 1206.81 | OK | |
| r-release-linux-x86_64 | 0.8.1 | 7.10 | 1196.65 | 1203.75 | OK | |
| r-release-macos-arm64 | 0.8.1 | 305.00 | OK | |||
| r-release-macos-x86_64 | 0.8.1 | 491.00 | OK | |||
| r-release-windows-x86_64 | 0.8.1 | 9.00 | 810.00 | 819.00 | OK | |
| r-oldrel-macos-arm64 | 0.8.1 | 388.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.8.1 | 543.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.8.1 | 10.00 | 1049.00 | 1059.00 | OK |
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [1035s/541s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 3 | WARN 40 | SKIP 72 | PASS 134 ]
══ Skipped tests (72) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
• empty test (1): 'test-tables.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
[ FAIL 3 | WARN 40 | SKIP 72 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [969s/544s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 3 | WARN 40 | SKIP 72 | PASS 134 ]
══ Skipped tests (72) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
• empty test (1): 'test-tables.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
[ FAIL 3 | WARN 40 | SKIP 72 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc