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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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(OmopSketch) > > test_check("OmopSketch") Starting 2 test processes. > test-databaseCharacteristics.R: The characterisation will focus on the following OMOP tables: visit_occurrence, condition_occurrence, drug_exposure, procedure_occurrence, measurement, and observation > test-databaseCharacteristics.R: The cdm is sampled to 20 > test-databaseCharacteristics.R: > Getting cdm snapshot > test-databaseCharacteristics.R: > Getting population characteristics > test-databaseCharacteristics.R: i Building new trimmed cohort > test-databaseCharacteristics.R: Creating initial cohort > test-databaseCharacteristics.R: v Cohort trimmed > test-databaseCharacteristics.R: i adding demographics columns > test-databaseCharacteristics.R: i summarising data > test-databaseCharacteristics.R: i summarising cohort general_population > test-databaseCharacteristics.R: v summariseCharacteristics finished! > test-databaseCharacteristics.R: > Summarising person table > test-databaseCharacteristics.R: > Summarising concept id counts > test-databaseCharacteristics.R: > Summarising clinical records > test-databaseCharacteristics.R: i Adding variables of interest to visit_occurrence. > test-databaseCharacteristics.R: i Summarising records per person in visit_occurrence. > test-databaseCharacteristics.R: i Summarising subjects not in person table in visit_occurrence. > test-databaseCharacteristics.R: i Summarising records in observation in visit_occurrence. > test-databaseCharacteristics.R: i Summarising records with start before birth date in visit_occurrence. > test-databaseCharacteristics.R: i Summarising records with end date before start date in visit_occurrence. > test-databaseCharacteristics.R: i Summarising domains in visit_occurrence. > test-databaseCharacteristics.R: i Summarising standard concepts in visit_occurrence. > test-databaseCharacteristics.R: i Summarising source vocabularies in visit_occurrence. > test-databaseCharacteristics.R: i Summarising concept types in visit_occurrence. > test-databaseCharacteristics.R: i Summarising missing data in visit_occurrence. > test-databaseCharacteristics.R: i Adding variables of interest to condition_occurrence. > test-databaseCharacteristics.R: i Summarising records per person in condition_occurrence. > test-databaseCharacteristics.R: i Summarising subjects not in person table in condition_occurrence. > test-databaseCharacteristics.R: i Summarising records in observation in condition_occurrence. > test-databaseCharacteristics.R: i Summarising records with start before birth date in condition_occurrence. > test-databaseCharacteristics.R: i Summarising records with end date before start date in condition_occurrence. > test-databaseCharacteristics.R: i Summarising domains in condition_occurrence. > test-databaseCharacteristics.R: i Summarising standard concepts in condition_occurrence. > test-databaseCharacteristics.R: i Summarising source vocabularies in condition_occurrence. > test-databaseCharacteristics.R: i Summarising concept types in condition_occurrence. > test-databaseCharacteristics.R: i Summarising missing data in condition_occurrence. > test-databaseCharacteristics.R: i Adding variables of interest to drug_exposure. > test-databaseCharacteristics.R: i Summarising records per person in drug_exposure. > test-databaseCharacteristics.R: i Summarising subjects not in person table in drug_exposure. > test-databaseCharacteristics.R: i Summarising records in observation in drug_exposure. > test-databaseCharacteristics.R: i Summarising records with start before birth date in drug_exposure. > test-databaseCharacteristics.R: i Summarising records with end date before start date in drug_exposure. > test-databaseCharacteristics.R: i Summarising domains in drug_exposure. > test-databaseCharacteristics.R: i Summarising standard concepts in drug_exposure. > test-databaseCharacteristics.R: i Summarising source vocabularies in drug_exposure. > test-databaseCharacteristics.R: i Summarising concept types in drug_exposure. > test-databaseCharacteristics.R: i Summarising concept class in drug_exposure. > test-databaseCharacteristics.R: i Summarising missing data in drug_exposure. > test-databaseCharacteristics.R: i Adding variables of interest to procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records per person in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising subjects not in person table in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records in observation in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records with start before birth date in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records with end date before start date in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising domains in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising standard concepts in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising source vocabularies in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising concept types in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising missing data in procedure_occurrence. > test-databaseCharacteristics.R: i Adding variables of interest to measurement. > test-databaseCharacteristics.R: i Summarising records per person in measurement. > test-databaseCharacteristics.R: i Summarising subjects not in person table in measurement. > test-databaseCharacteristics.R: i Summarising records in observation in measurement. > test-databaseCharacteristics.R: i Summarising records with start before birth date in measurement. > test-databaseCharacteristics.R: i Summarising records with end date before start date in measurement. > test-databaseCharacteristics.R: i Summarising domains in measurement. > test-databaseCharacteristics.R: i Summarising standard concepts in measurement. > test-databaseCharacteristics.R: i Summarising source vocabularies in measurement. > test-databaseCharacteristics.R: i Summarising concept types in measurement. > test-databaseCharacteristics.R: i Summarising missing data in measurement. > test-databaseCharacteristics.R: i Adding variables of interest to observation. > test-databaseCharacteristics.R: i Summarising records per person in observation. > test-databaseCharacteristics.R: i Summarising subjects not in person table in observation. > test-databaseCharacteristics.R: i Summarising records in observation in observation. > test-databaseCharacteristics.R: i Summarising records with start before birth date in observation. > test-databaseCharacteristics.R: i Summarising records with end date before start date in observation. > test-databaseCharacteristics.R: i Summarising domains in observation. > test-databaseCharacteristics.R: i Summarising standard concepts in observation. > test-databaseCharacteristics.R: i Summarising source vocabularies in observation. > test-databaseCharacteristics.R: i Summarising concept types in observation. > test-databaseCharacteristics.R: i Summarising missing data in observation. > test-databaseCharacteristics.R: > Summarising observation period > test-databaseCharacteristics.R: > Summarising trends: records, subjects, person-days, age and sex > test-databaseCharacteristics.R: > The number of person-days is not computed for event tables > test-databaseCharacteristics.R: :) Database characterisation finished. Code ran in 0 min and 55 sec > test-databaseCharacteristics.R: i 1 table created: "person_sample". > test-databaseCharacteristics.R: i Building new trimmed cohort > test-databaseCharacteristics.R: Adding demographics information > test-databaseCharacteristics.R: Creating initial cohort > test-databaseCharacteristics.R: Trim sex > test-databaseCharacteristics.R: v Cohort trimmed > test-databaseCharacteristics.R: The characterisation will focus on the following OMOP tables: visit_occurrence, condition_occurrence, drug_exposure, procedure_occurrence, measurement, and observation > test-databaseCharacteristics.R: The cdm is sampled to adult_males > test-databaseCharacteristics.R: > Getting cdm snapshot > test-databaseCharacteristics.R: > Getting population characteristics > test-databaseCharacteristics.R: i Building new trimmed cohort > test-databaseCharacteristics.R: Creating initial cohort > test-databaseCharacteristics.R: v Cohort trimmed > test-databaseCharacteristics.R: i adding demographics columns > test-databaseCharacteristics.R: i summarising data > test-databaseCharacteristics.R: i summarising cohort general_population > test-databaseCharacteristics.R: v summariseCharacteristics finished! > test-databaseCharacteristics.R: > Summarising person table > test-databaseCharacteristics.R: > Summarising concept id counts > test-databaseCharacteristics.R: > Summarising clinical records > test-databaseCharacteristics.R: i Adding variables of interest to visit_occurrence. > test-databaseCharacteristics.R: i Summarising records per person in visit_occurrence. > test-databaseCharacteristics.R: i Summarising subjects not in person table in visit_occurrence. > test-databaseCharacteristics.R: i Summarising records in observation in visit_occurrence. > test-databaseCharacteristics.R: i Summarising records with start before birth date in visit_occurrence. > test-databaseCharacteristics.R: i Summarising records with end date before start date in visit_occurrence. > test-databaseCharacteristics.R: i Summarising domains in visit_occurrence. > test-databaseCharacteristics.R: i Summarising standard concepts in visit_occurrence. > test-databaseCharacteristics.R: i Summarising source vocabularies in visit_occurrence. > test-databaseCharacteristics.R: i Summarising concept types in visit_occurrence. > test-databaseCharacteristics.R: i Summarising missing data in visit_occurrence. > test-databaseCharacteristics.R: i Adding variables of interest to condition_occurrence. > test-databaseCharacteristics.R: i Summarising records per person in condition_occurrence. > test-databaseCharacteristics.R: i Summarising subjects not in person table in condition_occurrence. > test-databaseCharacteristics.R: i Summarising records in observation in condition_occurrence. > test-databaseCharacteristics.R: i Summarising records with start before birth date in condition_occurrence. > test-databaseCharacteristics.R: i Summarising records with end date before start date in condition_occurrence. > test-databaseCharacteristics.R: i Summarising domains in condition_occurrence. > test-databaseCharacteristics.R: i Summarising standard concepts in condition_occurrence. > test-databaseCharacteristics.R: i Summarising source vocabularies in condition_occurrence. > test-databaseCharacteristics.R: i Summarising concept types in condition_occurrence. > test-databaseCharacteristics.R: i Summarising missing data in condition_occurrence. > test-databaseCharacteristics.R: i Adding variables of interest to drug_exposure. > test-databaseCharacteristics.R: i Summarising records per person in drug_exposure. > test-databaseCharacteristics.R: i Summarising subjects not in person table in drug_exposure. > test-databaseCharacteristics.R: i Summarising records in observation in drug_exposure. > test-databaseCharacteristics.R: i Summarising records with start before birth date in drug_exposure. > test-databaseCharacteristics.R: i Summarising records with end date before start date in drug_exposure. > test-databaseCharacteristics.R: i Summarising domains in drug_exposure. > test-databaseCharacteristics.R: i Summarising standard concepts in drug_exposure. > test-databaseCharacteristics.R: i Summarising source vocabularies in drug_exposure. > test-databaseCharacteristics.R: i Summarising concept types in drug_exposure. > test-databaseCharacteristics.R: i Summarising concept class in drug_exposure. > test-databaseCharacteristics.R: i Summarising missing data in drug_exposure. > test-databaseCharacteristics.R: i Adding variables of interest to procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records per person in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising subjects not in person table in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records in observation in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records with start before birth date in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising records with end date before start date in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising domains in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising standard concepts in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising source vocabularies in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising concept types in procedure_occurrence. > test-databaseCharacteristics.R: i Summarising missing data in procedure_occurrence. > test-databaseCharacteristics.R: i Adding variables of interest to measurement. > test-databaseCharacteristics.R: i Summarising records per person in measurement. > test-databaseCharacteristics.R: i Summarising subjects not in person table in measurement. > test-databaseCharacteristics.R: i Summarising records in observation in measurement. > test-databaseCharacteristics.R: i Summarising records with start before birth date in measurement. > test-databaseCharacteristics.R: i Summarising records with end date before start date in measurement. > test-databaseCharacteristics.R: i Summarising domains in measurement. > test-databaseCharacteristics.R: i Summarising standard concepts in measurement. > test-databaseCharacteristics.R: i Summarising source vocabularies in measurement. > test-databaseCharacteristics.R: i Summarising concept types in measurement. > test-databaseCharacteristics.R: i Summarising missing data in measurement. > test-databaseCharacteristics.R: i Adding variables of interest to observation. > test-databaseCharacteristics.R: i Summarising records per person in observation. > test-databaseCharacteristics.R: i Summarising subjects not in person table in observation. > test-databaseCharacteristics.R: i Summarising records in observation in observation. > test-databaseCharacteristics.R: i Summarising records with start before birth date in observation. > test-databaseCharacteristics.R: i Summarising records with end date before start date in observation. > test-databaseCharacteristics.R: i Summarising domains in observation. > test-databaseCharacteristics.R: i Summarising standard concepts in observation. > test-databaseCharacteristics.R: i Summarising source vocabularies in observation. > test-databaseCharacteristics.R: i Summarising concept types in observation. > test-databaseCharacteristics.R: i Summarising missing data in observation. > test-databaseCharacteristics.R: > Summarising observation period > test-databaseCharacteristics.R: > Summarising trends: records, subjects, person-days, age and sex > test-databaseCharacteristics.R: > The number of person-days is not computed for event tables > test-databaseCharacteristics.R: :) Database characterisation finished. Code ran in 0 min and 54 sec [ FAIL 0 | WARN 0 | SKIP 46 | PASS 25 ] ══ Skipped tests (46) ══════════════════════════════════════════════════════════ • On CRAN (46): 'test-mockOmopSketch.R:2:3', 'test-restrictStudyPeriod.R:2:3', 'test-summariseClinicalRecords.R:2:3', 'test-summariseClinicalRecords.R:86:3', 'test-summariseClinicalRecords.R:197:3', 'test-summariseClinicalRecords.R:223:3', 'test-summariseClinicalRecords.R:243:3', 'test-summariseClinicalRecords.R:269:3', 'test-summariseClinicalRecords.R:327:3', 'test-summariseClinicalRecords.R:443:3', 'test-summariseConceptIdCounts.R:2:3', 'test-summariseConceptIdCounts.R:84:3', 'test-summariseConceptIdCounts.R:107:3', 'test-summariseConceptIdCounts.R:136:3', 'test-summariseConceptIdCounts.R:248:3', 'test-summariseConceptIdCounts.R:273:3', 'test-summariseConceptIdCounts.R:306:3', 'test-summariseMissingData.R:2:3', 'test-summariseMissingData.R:61:3', 'test-summariseMissingData.R:86:3', 'test-summariseMissingData.R:105:3', 'test-summariseMissingData.R:143:3', 'test-summariseMissingData.R:171:3', 'test-summariseMissingData.R:286:3', 'test-summariseMissingData.R:306:3', 'test-summariseObservationPeriod.R:2:3', 'test-summariseObservationPeriod.R:302:3', 'test-summariseObservationPeriod.R:459:3', 'test-summariseObservationPeriod.R:498:3', 'test-summariseObservationPeriod.R:522:3', 'test-summariseObservationPeriod.R:547:3', 'test-summariseOmopSnapshot.R:2:3', 'test-summarisePerson.R:2:3', 'test-summariseTrend.R:2:3', 'test-summariseTrend.R:107:3', 'test-summariseTrend.R:201:3', 'test-summariseTrend.R:275:3', 'test-summariseTrend.R:350:3', 'test-summariseTrend.R:434:3', 'test-summariseTrend.R:507:3', 'test-summariseTrend.R:671:3', 'test-summariseTrend.R:719:3', 'test-summariseTrend.R:742:3', 'test-summariseTrend.R:760:3', 'test-databaseCharacteristics.R:2:3', 'test-databaseCharacteristics.R:26:3' [ FAIL 0 | WARN 0 | SKIP 46 | PASS 25 ] > > proc.time() user system elapsed 4.00 0.25 137.67