CRAN Package Check Results for Package PatientProfiles

Last updated on 2025-02-26 14:54:25 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.3 7.12 184.78 191.90 ERROR
r-devel-linux-x86_64-debian-gcc 1.2.3 4.89 127.54 132.43 ERROR
r-devel-linux-x86_64-fedora-clang 1.2.3 350.83 ERROR
r-devel-linux-x86_64-fedora-gcc 1.2.3 334.91 ERROR
r-devel-macos-arm64 1.2.3 223.00 OK
r-devel-macos-x86_64 1.2.3 534.00 NOTE
r-devel-windows-x86_64 1.2.3 8.00 452.00 460.00 NOTE
r-patched-linux-x86_64 1.2.3 7.66 167.48 175.14 ERROR
r-release-linux-x86_64 1.2.3 6.83 173.78 180.61 ERROR
r-release-macos-arm64 1.2.3 208.00 OK
r-release-macos-x86_64 1.2.3 414.00 OK
r-release-windows-x86_64 1.2.3 8.00 436.00 444.00 OK
r-oldrel-macos-arm64 1.2.3 OK
r-oldrel-macos-x86_64 1.2.3 425.00 OK
r-oldrel-windows-x86_64 1.2.3 11.00 197.00 208.00 ERROR

Check Details

Version: 1.2.3
Check: DESCRIPTION meta-information
Result: NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘addCategories.R’ ‘addCohortIntersect.R’ ‘addConceptIntersect.R’ ‘addDeath.R’ ‘addDemographics.R’ ‘addDemographicsQuery.R’ ‘addIntersect.R’ ‘addObservationPeriodId.R’ ‘addTableIntersect.R’ ‘checks.R’ ‘formats.R’ ‘mockPatientProfiles.R’ ‘summariseResult.R’ ‘utilities.R’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-macos-x86_64, r-devel-windows-x86_64

Version: 1.2.3
Check: dependencies in R code
Result: WARN Missing or unexported object: ‘CDMConnector::cdm_from_con’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-oldrel-windows-x86_64

Version: 1.2.3
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [77s/56s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘cohort-intersect.Rmd’ using rmarkdown Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd) Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘cohort-intersect.Rmd’ --- re-building ‘concept-intersect.Rmd’ using rmarkdown Quitting from lines 36-40 [unnamed-chunk-2] (concept-intersect.Rmd) Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘concept-intersect.Rmd’ --- re-building ‘demographics.rmd’ using rmarkdown Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd) Error: processing vignette 'demographics.rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘demographics.rmd’ --- re-building ‘summarise.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd) Error: processing vignette 'summarise.Rmd' failed with diagnostics: error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': could not find function "eunomia_dir" --- failed re-building ‘summarise.Rmd’ --- re-building ‘table-intersect.Rmd’ using rmarkdown Quitting from lines 35-39 [unnamed-chunk-3] (table-intersect.Rmd) Error: processing vignette 'table-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘table-intersect.Rmd’ SUMMARY: processing the following files failed: ‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’ ‘summarise.Rmd’ ‘table-intersect.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.2.3
Check: DESCRIPTION meta-information
Result: NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘addAge.Rd’ ‘addAgeQuery.Rd’ ‘addCategories.R’ ‘addCategories.Rd’ ‘addCdmName.Rd’ ‘addCohortIntersect.R’ ‘addCohortIntersectCount.Rd’ ‘addCohortIntersectDate.Rd’ ‘addCohortIntersectDays.Rd’ ‘addCohortIntersectFlag.Rd’ ‘addCohortName.Rd’ ‘addConceptIntersect.R’ ‘addConceptIntersectCount.Rd’ ‘addConceptIntersectDate.Rd’ ‘addConceptIntersectDays.Rd’ ‘addConceptIntersectFlag.Rd’ ‘addDateOfBirth.Rd’ ‘addDateOfBirthQuery.Rd’ ‘addDeath.R’ ‘addDeathDate.Rd’ ‘addDeathDays.Rd’ ‘addDeathFlag.Rd’ ‘addDemographics.R’ ‘addDemographics.Rd’ ‘addDemographicsQuery.R’ ‘addDemographicsQuery.Rd’ ‘addFutureObservation.Rd’ ‘addFutureObservationQuery.Rd’ ‘addInObservation.Rd’ ‘addInObservationQuery.Rd’ ‘addIntersect.R’ ‘addObservationPeriodId.R’ ‘addObservationPeriodId.Rd’ ‘addObservationPeriodIdQuery.Rd’ ‘addPriorObservation.Rd’ ‘addPriorObservationQuery.Rd’ ‘addSex.Rd’ ‘addSexQuery.Rd’ ‘addTableIntersect.R’ ‘addTableIntersectCount.Rd’ ‘addTableIntersectDate.Rd’ ‘addTableIntersectDays.Rd’ ‘addTableIntersectField.Rd’ ‘addTableIntersectFlag.Rd’ ‘checks.R’ ‘formats.R’ ‘mockPatientProfiles.R’ ‘summariseResult.R’ ‘summariseResult.Rd’ ‘utilities.R’ Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.2.3
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [55s/35s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.3
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [133s/227s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘cohort-intersect.Rmd’ using rmarkdown Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd) Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘cohort-intersect.Rmd’ --- re-building ‘concept-intersect.Rmd’ using rmarkdown Quitting from lines 36-40 [unnamed-chunk-2] (concept-intersect.Rmd) Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘concept-intersect.Rmd’ --- re-building ‘demographics.rmd’ using rmarkdown Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd) Error: processing vignette 'demographics.rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘demographics.rmd’ --- re-building ‘summarise.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd) Error: processing vignette 'summarise.Rmd' failed with diagnostics: error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': could not find function "eunomia_dir" --- failed re-building ‘summarise.Rmd’ --- re-building ‘table-intersect.Rmd’ using rmarkdown Quitting from lines 35-39 [unnamed-chunk-3] (table-intersect.Rmd) Error: processing vignette 'table-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘table-intersect.Rmd’ SUMMARY: processing the following files failed: ‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’ ‘summarise.Rmd’ ‘table-intersect.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64

Version: 1.2.3
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [126s/183s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2.3
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [75s/53s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 1.2.3
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [72s/49s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 1.2.3
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [60s] 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(PatientProfiles) > > test_check("PatientProfiles") Starting 2 test processes [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64