Last updated on 2026-11-09 01:52:24 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.1 | 8.59 | 744.52 | 753.11 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.6.1 | 6.33 | 184.28 | 190.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.6.1 | OK | ||||
| r-devel-linux-x86_64-fedora-gcc | 1.6.1 | 480.46 | OK | |||
| r-devel-windows-x86_64 | 1.6.1 | 12.00 | 448.00 | 460.00 | OK | |
| r-patched-linux-x86_64 | 1.6.1 | OK | ||||
| r-release-linux-x86_64 | 1.6.1 | 8.17 | 702.67 | 710.84 | OK | |
| r-release-macos-arm64 | 1.6.1 | 2.00 | 118.00 | 120.00 | OK | |
| r-release-macos-x86_64 | 1.6.1 | 6.00 | 544.00 | 550.00 | OK | |
| r-release-windows-x86_64 | 1.6.1 | 11.00 | 433.00 | 444.00 | OK | |
| r-oldrel-macos-arm64 | 1.6.1 | 2.00 | 121.00 | 123.00 | OK | |
| r-oldrel-macos-x86_64 | 1.6.1 | 6.00 | 490.00 | 496.00 | OK | |
| r-oldrel-windows-x86_64 | 1.6.1 | 15.00 | 625.00 | 640.00 | OK |
Version: 1.6.1
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [71s/39s]
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.
> test-addCohortIntersect.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addCohortIntersect.R: i /home/hornik/tmp/scratch/RtmpO9Vu2u/duckdb
> test-addCohortIntersect.R: This is removed when the R session ends.
> test-addCohortIntersect.R: * Extensions are re-downloaded each session.
> test-addCohortIntersect.R: * Secrets are lost.
> test-addCohortIntersect.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addCohortIntersect.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addCohortIntersect.R: i See ?duckdb_storage for details and alternatives.
> test-addCohortEvent.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addCohortEvent.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addCohortEvent.R: This is removed when the R session ends.
> test-addCohortEvent.R: * Extensions are re-downloaded each session.
> test-addCohortEvent.R: * Secrets are lost.
> test-addCohortEvent.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addCohortEvent.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addCohortEvent.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addCohortEvent-50.R
> test-addCohortIntersect.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addCohortIntersect.R: i /home/hornik/tmp/scratch/RtmpO9Vu2u/duckdb
> test-addCohortIntersect.R: This is removed when the R session ends.
> test-addCohortIntersect.R: * Extensions are re-downloaded each session.
> test-addCohortIntersect.R: * Secrets are lost.
> test-addCohortIntersect.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addCohortIntersect.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addCohortIntersect.R: i See ?duckdb_storage for details and alternatives.
> test-addConceptEvent.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addConceptEvent.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addConceptEvent.R: This is removed when the R session ends.
> test-addConceptEvent.R: * Extensions are re-downloaded each session.
> test-addConceptEvent.R: * Secrets are lost.
> test-addConceptEvent.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addConceptEvent.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addConceptEvent.R: i See ?duckdb_storage for details and alternatives.
> test-addCohortIntersect.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addCohortIntersect.R: i /home/hornik/tmp/scratch/RtmpO9Vu2u/duckdb
> test-addCohortIntersect.R: This is removed when the R session ends.
> test-addCohortIntersect.R: * Extensions are re-downloaded each session.
> test-addCohortIntersect.R: * Secrets are lost.
> test-addCohortIntersect.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addCohortIntersect.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addCohortIntersect.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addCohortIntersect-8.R
Saving _problems/test-addCohortIntersect-100.R
Saving _problems/test-addCohortIntersect-213.R
> test-addConceptIntersect.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addConceptIntersect.R: i /home/hornik/tmp/scratch/RtmpO9Vu2u/duckdb
> test-addConceptIntersect.R: This is removed when the R session ends.
> test-addConceptIntersect.R: * Extensions are re-downloaded each session.
> test-addConceptIntersect.R: * Secrets are lost.
> test-addConceptIntersect.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addConceptIntersect.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addConceptIntersect.R: i See ?duckdb_storage for details and alternatives.
> test-addDeath.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDeath.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDeath.R: This is removed when the R session ends.
> test-addDeath.R: * Extensions are re-downloaded each session.
> test-addDeath.R: * Secrets are lost.
> test-addDeath.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDeath.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDeath.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addDeath-4.R
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
> test-addDemographics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addDemographics.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addDemographics.R: This is removed when the R session ends.
> test-addDemographics.R: * Extensions are re-downloaded each session.
> test-addDemographics.R: * Secrets are lost.
> test-addDemographics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addDemographics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addDemographics.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addDemographics-48.R
Saving _problems/test-addDemographics-107.R
Saving _problems/test-addDemographics-152.R
Saving _problems/test-addDemographics-254.R
Saving _problems/test-addDemographics-334.R
Saving _problems/test-addDemographics-553.R
Saving _problems/test-addDemographics-617.R
Saving _problems/test-addDemographics-672.R
Saving _problems/test-addDemographics-1404.R
> test-addInObservation.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addInObservation.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addInObservation.R: This is removed when the R session ends.
> test-addInObservation.R: * Extensions are re-downloaded each session.
> test-addInObservation.R: * Secrets are lost.
> test-addInObservation.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addInObservation.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addInObservation.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addInObservation-79.R
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
> test-addObservationPeriodId.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addObservationPeriodId.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addObservationPeriodId.R: This is removed when the R session ends.
> test-addObservationPeriodId.R: * Extensions are re-downloaded each session.
> test-addObservationPeriodId.R: * Secrets are lost.
> test-addObservationPeriodId.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addObservationPeriodId.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addObservationPeriodId.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addObservationPeriodId-195.R
> test-addTableIntersect.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addTableIntersect.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addTableIntersect.R: This is removed when the R session ends.
> test-addTableIntersect.R: * Extensions are re-downloaded each session.
> test-addTableIntersect.R: * Secrets are lost.
> test-addTableIntersect.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addTableIntersect.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addTableIntersect.R: i See ?duckdb_storage for details and alternatives.
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
> test-addTableIntersect.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-addTableIntersect.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-addTableIntersect.R: This is removed when the R session ends.
> test-addTableIntersect.R: * Extensions are re-downloaded each session.
> test-addTableIntersect.R: * Secrets are lost.
> test-addTableIntersect.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-addTableIntersect.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-addTableIntersect.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-addTableIntersect-3.R
Saving _problems/test-addTableIntersect-190.R
> test-class.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-class.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-class.R: This is removed when the R session ends.
> test-class.R: * Extensions are re-downloaded each session.
> test-class.R: * Secrets are lost.
> test-class.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-class.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-class.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-class-24.R
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
> test-summariseResult.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseResult.R: i /home/hornik/tmp/scratch/RtmpCHlyZ9/duckdb
> test-summariseResult.R: This is removed when the R session ends.
> test-summariseResult.R: * Extensions are re-downloaded each session.
> test-summariseResult.R: * Secrets are lost.
> test-summariseResult.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseResult.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseResult.R: i See ?duckdb_storage for details and alternatives.
> test-addConceptIntersect.R: ! The following columns will be overwritten:
> test-addConceptIntersect.R: * intersect
Saving _problems/test-summariseResult-3.R
[ FAIL 20 | WARN 8 | SKIP 135 | PASS 21 ]
══ Skipped tests (135) ═════════════════════════════════════════════════════════
• On CRAN (135): 'test-addAttributes.R:2:3', 'test-addBirthDay.R:2:3',
'test-addCategories.R:2:3', 'test-addCategories.R:70:3',
'test-addCategories.R:109:3', 'test-addCategories.R:157:3',
'test-addCohortEvent.R:95:3', 'test-addCohortEvent.R:126:3',
'test-addCohortEvent.R:152:3', 'test-addCohortEvent.R:176:3',
'test-addCohortEvent.R:227:3', 'test-addCohortIntersect.R:272:3',
'test-addCohortIntersect.R:347:3', 'test-addCohortIntersect.R:393:3',
'test-addCohortIntersect.R:502:3', 'test-addCohortIntersect.R:592:3',
'test-addCohortIntersect.R:650:3', 'test-addCohortIntersect.R:722:3',
'test-addCohortIntersect.R:744:3', 'test-addCohortIntersect.R:830:3',
'test-addCohortIntersect.R:884:3', 'test-addCohortIntersect.R:942:3',
'test-addCohortIntersect.R:1000:3', 'test-addConceptEvent.R:84:3',
'test-addConceptEvent.R:110:3', 'test-addDeath.R:101:3',
'test-addDeath.R:143:3', 'test-addDeath.R:241:3', 'test-addDeath.R:281:3',
'test-addDemographics.R:2:3', 'test-addDemographics.R:26:3',
'test-addDemographics.R:353:3', 'test-addDemographics.R:422:3',
'test-addDemographics.R:697:3', 'test-addDemographics.R:849:3',
'test-addDemographics.R:870:3', 'test-addDemographics.R:982:3',
'test-addDemographics.R:1058:3', 'test-addDemographics.R:1172:3',
'test-addDemographics.R:1238:3', 'test-addDemographics.R:1268:3',
'test-addDemographics.R:1298:3', 'test-addDemographics.R:1317:3',
'test-addDemographics.R:1331:3', 'test-addDemographics.R:1352:3',
'test-addDemographics.R:1382:3', 'test-addDemographics.R:1441:3',
'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:14:3',
'test-addFutureObservation.R:30:3', 'test-addFutureObservation.R:90:3',
'test-addFutureObservation.R:150:3', 'test-addFutureObservation.R:212:3',
'test-addFutureObservation.R:256:3', 'test-addInObservation.R:2:3',
'test-addInObservation.R:18:3', 'test-addInObservation.R:49:3',
'test-addInObservation.R:173:3', '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:855:3', 'test-addIntersect.R:872:3',
'test-addIntersect.R:942:3', 'test-addIntersect.R:1028:3',
'test-addIntersect.R:1209:3', 'test-addIntersect.R:1225:3',
'test-addIntersect.R:1273:3', 'test-addObservationPeriodId.R:2:3',
'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:14:3',
'test-addPriorObservation.R:30:3', 'test-addPriorObservation.R:76:3',
'test-addPriorObservation.R:121:3', 'test-addPriorObservation.R:184:3',
'test-addSex.R:2:3', 'test-addSex.R:16:3', 'test-addSex.R:33:3',
'test-addSex.R:76:3', 'test-addTableIntersect.R:48:3',
'test-addTableIntersect.R:233:3', 'test-addTableIntersect.R:341:3',
'test-addTableIntersect.R:477:3', 'test-addTableIntersect.R:608:3',
'test-benchmarkPatientProfiles.R:2:3', 'test-checks.R:2:3',
'test-checks.R:102:3', 'test-checks.R:155:3', 'test-checks.R:172:3',
'test-checks.R:222:3', 'test-checks.R:249:3', 'test-columnType.R:2:3',
'test-columnType.R:29:3', 'test-columnType.R:75:3',
'test-columnType.R:153:3', 'test-filterCohortId.R:2:3',
'test-filterInObservation.R:2:3', 'test-format.R:2:3', 'test-format.R:89:3',
'test-format.R:100:3', 'test-format.R:110:3', 'test-indexDate.R:2:3',
'test-indexDate.R:56:3', 'test-indexDate.R:90:3', 'test-indexDate.R:128:3',
'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3',
'test-summariseResult.R:132:3', 'test-summariseResult.R:218:3',
'test-summariseResult.R:257:3', 'test-summariseResult.R:284:3',
'test-summariseResult.R:329:3', 'test-summariseResult.R:394:3',
'test-summariseResult.R:438:3', 'test-summariseResult.R:460:3',
'test-summariseResult.R:531:3', 'test-summariseResult.R:619:3',
'test-summariseResult.R:777:3', 'test-summariseResult.R:880:3',
'test-summariseResult.R:1146:3', 'test-summariseResult.R:1159:3',
'test-utilities.R:2:3', 'test-addConceptIntersect.R:2:3',
'test-addConceptIntersect.R:100:3', 'test-addConceptIntersect.R:125:3',
'test-addConceptIntersect.R:177:3', 'test-addConceptIntersect.R:224:3',
'test-addConceptIntersect.R:265:3', 'test-addConceptIntersect.R:298:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-addCohortEvent.R:50:3'): event days returns events and observation boundaries ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─PatientProfiles (local) cohortEventTestCdm() at test-addCohortEvent.R:50:3
2. ├─base::suppressWarnings(...) at test-addCohortEvent.R:38:3
3. │ └─base::withCallingHandlers(...)
4. ├─PatientProfiles:::copyCdm(...)
5. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
6. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
7. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
8. │ ├─omopgenerics:::checkEmpty(...)
9. │ ├─omopgenerics:::checkClass(...)
10. │ ├─omopgenerics:::checkLength(...)
11. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
12. │ └─omopgenerics:::createCheckObject(x)
13. └─PatientProfiles::mockPatientProfiles(...)
14. ├─base::suppressWarnings(...)
15. │ └─base::withCallingHandlers(...)
16. ├─base::suppressMessages(...)
17. │ └─base::withCallingHandlers(...)
18. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
19. └─omock::mockVocabularySet(...)
20. └─omock:::readTables(tmpFolder, cv, vocab = T)
21. ├─omock:::castColumns(...)
22. │ ├─dplyr::filter(...)
23. │ ├─dplyr:::filter.data.frame(...)
24. │ │ └─dplyr:::filter_impl(...)
25. │ │ └─dplyr:::dplyr_quosures(...)
26. │ │ └─rlang::quos(..., .ignore_empty = "all")
27. │ └─base::colnames(x)
28. │ └─base::is.data.frame(x)
29. └─arrow::read_parquet(file = tables[[nm]])
30. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
31. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
32. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
33. │ │ └─assertthat::see_if(..., env = env, msg = msg)
34. │ │ ├─base::tryCatch(...)
35. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
36. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
37. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
38. │ │ └─base::eval(assertion, env)
39. │ │ └─base::eval(assertion, env)
40. │ └─base::inherits(object, class)
41. └─ParquetArrowReaderProperties$create()
42. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addCohortIntersect.R:7:3'): output format - one outcome cohort ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addCohortIntersect.R:7:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addCohortIntersect.R:96:3'): first vs last event - cohort table ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addCohortIntersect.R:96:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addCohortIntersect.R:209:3'): multiple cohort entries per person ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addCohortIntersect.R:209:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDeath.R:3:3'): addDeathDate ─────────────────────────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDeath.R:3:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:47:3'): addDemographics, cohort and condition_occurrence ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:47:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:82:3'): addDemographics, parameters ──────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-addDemographics.R:82:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─PatientProfiles:::copyCdm(...)
8. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
9. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
10. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
11. │ ├─omopgenerics:::checkEmpty(...)
12. │ ├─omopgenerics:::checkClass(...)
13. │ ├─omopgenerics:::checkLength(...)
14. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
15. │ └─omopgenerics:::createCheckObject(x)
16. └─PatientProfiles::mockPatientProfiles(...)
17. ├─base::suppressWarnings(...)
18. │ └─base::withCallingHandlers(...)
19. ├─base::suppressMessages(...)
20. │ └─base::withCallingHandlers(...)
21. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
22. └─omock::mockVocabularySet(...)
23. └─omock:::readTables(tmpFolder, cv, vocab = T)
24. ├─omock:::castColumns(...)
25. │ ├─dplyr::filter(...)
26. │ ├─dplyr:::filter.data.frame(...)
27. │ │ └─dplyr:::filter_impl(...)
28. │ │ └─dplyr:::dplyr_quosures(...)
29. │ │ └─rlang::quos(..., .ignore_empty = "all")
30. │ └─base::colnames(x)
31. │ └─base::is.data.frame(x)
32. └─arrow::read_parquet(file = tables[[nm]])
33. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
34. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
35. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
36. │ │ └─assertthat::see_if(..., env = env, msg = msg)
37. │ │ ├─base::tryCatch(...)
38. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
39. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
40. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
41. │ │ └─base::eval(assertion, env)
42. │ │ └─base::eval(assertion, env)
43. │ └─base::inherits(object, class)
44. └─ParquetArrowReaderProperties$create()
45. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:151:3'): partial demographics - cohorts ──────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:151:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:253:3'): partial demographics - omop tables ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:253:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:323:3'): priorObservation and future_observation - outside of observation period ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:323:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:546:3'): age at cohort end, no missing, check age computation ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:546:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:610:3'): age at cohort entry, missing year/month/day of birth ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:610:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:665:3'): multiple cohortIds, check age at cohort end ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addDemographics.R:665:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addDemographics.R:1403:3'): test query functions ───────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(mockPatientProfiles(source = "local")) at test-addDemographics.R:1403:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(source = "local")
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addInObservation.R:63:3'): addInObservation, window ────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-addInObservation.R:63:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─PatientProfiles:::copyCdm(...)
8. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
9. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
10. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
11. │ ├─omopgenerics:::checkEmpty(...)
12. │ ├─omopgenerics:::checkClass(...)
13. │ ├─omopgenerics:::checkLength(...)
14. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
15. │ └─omopgenerics:::createCheckObject(x)
16. └─PatientProfiles::mockPatientProfiles(...)
17. ├─base::suppressWarnings(...)
18. │ └─base::withCallingHandlers(...)
19. ├─base::suppressMessages(...)
20. │ └─base::withCallingHandlers(...)
21. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
22. └─omock::mockVocabularySet(...)
23. └─omock:::readTables(tmpFolder, cv, vocab = T)
24. ├─omock:::castColumns(...)
25. │ ├─dplyr::filter(...)
26. │ ├─dplyr:::filter.data.frame(...)
27. │ │ └─dplyr:::filter_impl(...)
28. │ │ └─dplyr:::dplyr_quosures(...)
29. │ │ └─rlang::quos(..., .ignore_empty = "all")
30. │ └─base::colnames(x)
31. │ └─base::is.data.frame(x)
32. └─arrow::read_parquet(file = tables[[nm]])
33. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
34. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
35. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
36. │ │ └─assertthat::see_if(..., env = env, msg = msg)
37. │ │ ├─base::tryCatch(...)
38. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
39. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
40. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
41. │ │ └─base::eval(assertion, env)
42. │ │ └─base::eval(assertion, env)
43. │ └─base::inherits(object, class)
44. └─ParquetArrowReaderProperties$create()
45. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addObservationPeriodId.R:190:3'): check when there is the same record in multiple cohorts ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addObservationPeriodId.R:190:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addTableIntersect.R:2:3'): basic structures ────────────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(mockPatientProfiles(source = "local")) at test-addTableIntersect.R:2:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(source = "local")
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-addTableIntersect.R:185:3'): addTableIntersectCount example ────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(...) at test-addTableIntersect.R:185:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-class.R:19:3'): test class consistency across cohort operations ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-class.R:19:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─PatientProfiles:::copyCdm(...)
8. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
9. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
10. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
11. │ ├─omopgenerics:::checkEmpty(...)
12. │ ├─omopgenerics:::checkClass(...)
13. │ ├─omopgenerics:::checkLength(...)
14. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
15. │ └─omopgenerics:::createCheckObject(x)
16. └─PatientProfiles::mockPatientProfiles(...)
17. ├─base::suppressWarnings(...)
18. │ └─base::withCallingHandlers(...)
19. ├─base::suppressMessages(...)
20. │ └─base::withCallingHandlers(...)
21. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
22. └─omock::mockVocabularySet(...)
23. └─omock:::readTables(tmpFolder, cv, vocab = T)
24. ├─omock:::castColumns(...)
25. │ ├─dplyr::filter(...)
26. │ ├─dplyr:::filter.data.frame(...)
27. │ │ └─dplyr:::filter_impl(...)
28. │ │ └─dplyr:::dplyr_quosures(...)
29. │ │ └─rlang::quos(..., .ignore_empty = "all")
30. │ └─base::colnames(x)
31. │ └─base::is.data.frame(x)
32. └─arrow::read_parquet(file = tables[[nm]])
33. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
34. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
35. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
36. │ │ └─assertthat::see_if(..., env = env, msg = msg)
37. │ │ ├─base::tryCatch(...)
38. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
39. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
40. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
41. │ │ └─base::eval(assertion, env)
42. │ │ └─base::eval(assertion, env)
43. │ └─base::inherits(object, class)
44. └─ParquetArrowReaderProperties$create()
45. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseResult.R:2:3'): test all functions ────────────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─PatientProfiles:::copyCdm(mockPatientProfiles(source = "local")) at test-summariseResult.R:2:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:48:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles::mockPatientProfiles(source = "local")
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
[ FAIL 20 | WARN 8 | SKIP 135 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.6.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
Quitting from cohort-intersect.Rmd:22-36 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `parquet___arrow___ArrowReaderProperties__Make()`:
! Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
---
Backtrace:
▆
1. └─PatientProfiles::mockPatientProfiles(...)
2. ├─base::suppressWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. ├─base::suppressMessages(...)
5. │ └─base::withCallingHandlers(...)
6. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
7. └─omock::mockVocabularySet(...)
8. └─omock:::readTables(tmpFolder, cv, vocab = T)
9. ├─omock:::castColumns(...)
10. │ ├─dplyr::filter(...)
11. │ ├─dplyr:::filter.data.frame(...)
12. │ │ └─dplyr:::filter_impl(...)
13. │ │ └─dplyr:::dplyr_quosures(...)
14. │ │ └─rlang::quos(..., .ignore_empty = "all")
15. │ └─base::colnames(x)
16. │ └─base::is.data.frame(x)
17. └─arrow::read_parquet(file = tables[[nm]])
18. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
19. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
20. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
21. │ │ └─assertthat::see_if(..., env = env, msg = msg)
22. │ │ ├─base::tryCatch(...)
23. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
24. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
25. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
26. │ │ └─base::eval(assertion, env)
27. │ │ └─base::eval(assertion, env)
28. │ └─base::inherits(object, class)
29. └─ParquetArrowReaderProperties$create()
30. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics:
Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
--- failed re-building ‘cohort-intersect.Rmd’
--- re-building ‘demographics.rmd’ using rmarkdown
Quitting from demographics.rmd:19-28 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `parquet___arrow___ArrowReaderProperties__Make()`:
! Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
---
Backtrace:
▆
1. └─PatientProfiles::mockPatientProfiles(...)
2. ├─base::suppressWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. ├─base::suppressMessages(...)
5. │ └─base::withCallingHandlers(...)
6. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
7. └─omock::mockVocabularySet(...)
8. └─omock:::readTables(tmpFolder, cv, vocab = T)
9. ├─omock:::castColumns(...)
10. │ ├─dplyr::filter(...)
11. │ ├─dplyr:::filter.data.frame(...)
12. │ │ └─dplyr:::filter_impl(...)
13. │ │ └─dplyr:::dplyr_quosures(...)
14. │ │ └─rlang::quos(..., .ignore_empty = "all")
15. │ └─base::colnames(x)
16. │ └─base::is.data.frame(x)
17. └─arrow::read_parquet(file = tables[[nm]])
18. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
19. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
20. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
21. │ │ └─assertthat::see_if(..., env = env, msg = msg)
22. │ │ ├─base::tryCatch(...)
23. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
24. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
25. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
26. │ │ └─base::eval(assertion, env)
27. │ │ └─base::eval(assertion, env)
28. │ └─base::inherits(object, class)
29. └─ParquetArrowReaderProperties$create()
30. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'demographics.rmd' failed with diagnostics:
Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
--- failed re-building ‘demographics.rmd’
--- re-building ‘event.rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘event.rmd’
SUMMARY: processing the following files failed:
‘cohort-intersect.Rmd’ ‘demographics.rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc