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Type 'q()' to quit R. > # 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: - 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-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-estimateSurvival.R: Getting overall estimates > test-plotSurvival.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-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 survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort' > test-plotSurvival.R: - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort 'death_cohort' > 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 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', 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. > 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-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-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_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: ========================>------ 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' and outcome cohort 'progression' > test-estimateSurvival.R: Getting overall estimates > 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: ========================>------ 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: ==================>------------ 60% | 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: ==================>------------ 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: ========================>------ 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. [ FAIL 0 | WARN 10 | SKIP 56 | PASS 70 ] ══ 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' [ FAIL 0 | WARN 10 | SKIP 56 | PASS 70 ] > > proc.time() user system elapsed 7.84 0.39 258.20