Last updated on 2025-12-07 04:49:47 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 6.28 | 1084.13 | 1090.41 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 4.78 | 462.12 | 466.90 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 52.00 | 1732.70 | 1784.70 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 23.00 | 1640.93 | 1663.93 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 9.00 | 678.00 | 687.00 | OK | |
| r-patched-linux-x86_64 | 1.0.3 | 7.03 | 1042.21 | 1049.24 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 6.12 | 991.33 | 997.45 | OK | |
| r-release-macos-arm64 | 1.1.0 | 2.00 | 155.00 | 157.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 7.00 | 618.00 | 625.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 11.00 | 666.00 | 677.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 2.00 | 150.00 | 152.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.0 | 7.00 | 577.00 | 584.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 11.00 | 811.00 | 822.00 | OK |
Version: 1.1.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'roxygen2', 'knitr', 'rmarkdown', 'gt', 'flextable', 'visOmopResults'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘CohortSurvival-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optionsTableSurvival
> ### Title: Additional arguments for the function tableSurvival()
> ### Aliases: optionsTableSurvival
>
> ### ** Examples
>
> {
+ optionsTableSurvival()
+ }
Error in loadNamespace(x) : there is no package called ‘visOmopResults’
Calls: optionsTableSurvival ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [427s/320s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortSurvival)
>
> test_check("CohortSurvival")
Starting 2 test processes.
> test-estimateSurvival.R: ==================>------------ 60% | ETA: 2s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-plotSurvival.R: ==================>------------ 60% | ETA: 2s
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-plotSurvival.R: Getting overall estimates
> test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-plotSurvival.R: Getting overall estimates
> test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ==================>------------ 60% | ETA: 2s
> test-plotSurvival.R: ==================>------------ 60% | ETA: 2s
> test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-plotSurvival.R: Getting overall estimates
> test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_test_empty'
> test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-plotSurvival.R: Getting overall estimates
> test-plotSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
Saving _problems/test-plotSurvival-179.R
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression_fake_empty' and competing outcome cohort 'death_cohort'
> test-reexports-omopgenerics.R: ========================>------ 80% | ETA: 1s
> test-reexports-omopgenerics.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-reexports-omopgenerics.R: Getting overall estimates
> test-reexports-omopgenerics.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-reexports-omopgenerics.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R:
> test-estimateSurvival.R: -- No results for competing risk analysis --------------------------------------
> test-estimateSurvival.R: Competing risk variable must have three levels.Do you have at least 1
> test-estimateSurvival.R: individual for:
> test-estimateSurvival.R: * 1) censored without event,
> test-estimateSurvival.R: * 2) censored at outcome event of intest, and
> test-estimateSurvival.R: * 3) censored at outcome competing event?
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_test_empty'
> test-estimateSurvival.R:
> test-estimateSurvival.R: -- No results for competing risk analysis --------------------------------------
> test-estimateSurvival.R: Competing risk variable must have three levels.Do you have at least 1
> test-estimateSurvival.R: individual for:
> test-estimateSurvival.R: * 1) censored without event,
> test-estimateSurvival.R: * 2) censored at outcome event of intest, and
> test-estimateSurvival.R: * 3) censored at outcome competing event?
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression_fake_empty' and competing outcome cohort 'death_test_empty'
> test-reexports-omopgenerics.R: Getting overall estimates
> test-reexports-omopgenerics.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R:
> test-estimateSurvival.R: -- No results for competing risk analysis --------------------------------------
> test-estimateSurvival.R: Competing risk variable must have three levels.Do you have at least 1
> test-estimateSurvival.R: individual for:
> test-estimateSurvival.R: * 1) censored without event,
> test-estimateSurvival.R: * 2) censored at outcome event of intest, and
> test-estimateSurvival.R: * 3) censored at outcome competing event?
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ==================>------------ 60% | ETA: 2s
> test-estimateSurvival.R: ========================>------ 80% | ETA: 2s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ==================>------------ 60% | ETA: 2s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ========================>------ 80% | ETA: 1s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ========================>------ 80% | ETA: 1s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: `eventgap` eliminated from settings as all elements are NA.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: `eventgap` eliminated from settings as all elements are NA.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis_2020' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis_2020', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ========================>------ 80% | ETA: 1s
> test-estimateSurvival.R: ========================>------ 80% | ETA: 1s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: ========================>------ 80% | ETA: 1s
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
> test-estimateSurvival.R: - Getting survival for target cohort 'mgus_diagnosis', outcome cohort 'progression' and competing outcome cohort 'death_cohort'
> test-estimateSurvival.R: Getting overall estimates
> test-estimateSurvival.R: `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and `minimum_survival_days` casted to character.
Saving _problems/test-estimateSurvival-2255.R
[ FAIL 2 | WARN 8 | SKIP 56 | PASS 62 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test-asSurvivalResult.R:2:3', 'test-asSurvivalResult.R:19:3',
'test-asSurvivalResult.R:54:3', 'test-asSurvivalResult.R:94:3',
'test-asSurvivalResult.R:148:3', 'test-asSurvivalResult.R:203:3',
'test-asSurvivalResult.R:246:3', 'test-asSurvivalResult.R:289:3',
'test-asSurvivalResult.R:330:3', 'test-addCohortSurvival.R:2:3',
'test-addCohortSurvival.R:73:3', 'test-addCohortSurvival.R:160:3',
'test-addCohortSurvival.R:259:3', 'test-addCohortSurvival.R:351:3',
'test-addCohortSurvival.R:455:3', 'test-addCohortSurvival.R:541:3',
'test-addCohortSurvival.R:633:3', 'test-addCohortSurvival.R:712:3',
'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3',
'test-plotSurvival.R:19:3', 'test-plotSurvival.R:52:3',
'test-plotSurvival.R:83:3', 'test-plotSurvival.R:126:3',
'test-plotSurvival.R:134:3', 'test-plotSurvival.R:157:3',
'test-plotSurvival.R:186:3', 'test-reexports-omopgenerics.R:3:3',
'test-riskTable.R:2:3', 'test-riskTable.R:65:3', 'test-tableSurvival.R:2:3',
'test-tableSurvival.R:91:3', 'test-tableSurvival.R:117:3',
'test-tableSurvival.R:141:3', 'test-tableSurvival.R:151:3',
'test-tableSurvivalAttrition.R:2:3', 'test-estimateSurvival.R:80:3',
'test-estimateSurvival.R:131:3', 'test-estimateSurvival.R:193:3',
'test-estimateSurvival.R:351:3', 'test-estimateSurvival.R:556:3',
'test-estimateSurvival.R:698:3', 'test-estimateSurvival.R:1166:3',
'test-estimateSurvival.R:1278:3', 'test-estimateSurvival.R:1300:3',
'test-estimateSurvival.R:1367:3', 'test-estimateSurvival.R:1552:3',
'test-estimateSurvival.R:1665:3', 'test-estimateSurvival.R:1695:3',
'test-estimateSurvival.R:1714:3', 'test-estimateSurvival.R:1747:3',
'test-estimateSurvival.R:1876:3', 'test-estimateSurvival.R:2090:3',
'test-estimateSurvival.R:2222:5', 'test-estimateSurvival.R:2435:3',
'test-estimateSurvival.R:2467:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotSurvival.R:179:3'): plot with bound results with different hidden inputs ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `plotSurvival(surv_all, colour = "follow_up_days")`: The package "visOmopResults" is required.
Backtrace:
▆
1. ├─testthat::expect_warning(plotSurvival(surv_all, colour = "follow_up_days")) at test-plotSurvival.R:179:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─CohortSurvival::plotSurvival(surv_all, colour = "follow_up_days")
8. └─rlang::check_installed("visOmopResults")
── Error ('test-estimateSurvival.R:2253:5'): no outcomes among cohort ──────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `tableSurvival(surv, type = "tibble")`: The package "visOmopResults" (>= 0.5.0) is required.
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-estimateSurvival.R:2253:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::pull(tableSurvival(surv, type = "tibble"), `[header_name]Estimate name\n[header_level]Number events`)
5. └─CohortSurvival::tableSurvival(surv, type = "tibble")
6. └─rlang::check_installed("visOmopResults", version = "0.5.0")
[ FAIL 2 | WARN 8 | SKIP 56 | PASS 62 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc