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 |
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