Last updated on 2025-02-16 10:50:43 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.7.0 | 10.58 | 535.69 | 546.27 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.7.0 | 7.45 | 381.92 | 389.37 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.7.0 | 886.77 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.7.0 | 810.47 | NOTE | |||
| r-devel-macos-arm64 | 1.7.0 | 203.00 | OK | |||
| r-devel-macos-x86_64 | 1.7.0 | 468.00 | NOTE | |||
| r-devel-windows-x86_64 | 1.7.0 | 10.00 | 457.00 | 467.00 | ERROR | |
| r-patched-linux-x86_64 | 1.7.0 | 10.14 | 506.19 | 516.33 | ERROR | |
| r-release-linux-x86_64 | 1.7.0 | 9.82 | 512.52 | 522.34 | ERROR | |
| r-release-macos-arm64 | 1.7.0 | 204.00 | OK | |||
| r-release-macos-x86_64 | 1.7.0 | 355.00 | OK | |||
| r-release-windows-x86_64 | 1.7.0 | 10.00 | 437.00 | 447.00 | OK | |
| r-oldrel-macos-arm64 | 1.7.0 | 220.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.7.0 | 379.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.7.0 | 15.00 | 572.00 | 587.00 | OK |
Version: 1.7.0
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:
‘benchmarkCDMConnector.R’ ‘cdm.R’ ‘cdmSubset.R’ ‘copy_cdm_to.R’
‘dbSource.R’ ‘generateCohortSet.R’ ‘generateConceptCohortSet.R’
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-devel-macos-x86_64, r-devel-windows-x86_64
Version: 1.7.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [286s/342s]
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(CDMConnector)
>
> test_check("CDMConnector")
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /tmp/RtmpYeM9eh/file25a56c6c1234ad/GiBleed_5.3.zip
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
Support for 'prefix' in writeSchema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead.
This message is displayed once per session.
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.1s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [270ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [388ms]
i Generating 3 cohorts
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [860ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [461ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [379ms]
i Generating 3 cohorts
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [406ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [303ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [330ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [416ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [357ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [362ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default
v Generating cohort (1/1) - gibleed_default [294ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default_with_descendants
v Generating cohort (1/1) - gibleed_default_with_descendants [383ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [420ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [360ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [213ms]
Attaching package: 'clock'
The following object is masked from 'package:CDMConnector':
as_date
===============>--------------- 52% | ETA: 2s
=====================>--------- 70% | ETA: 1s
! cdm name not specified and could not be inferred from the cdm source table
i Generating 5 cohorts
i Generating cohort (1/5) - gibleed_all
v Generating cohort (1/5) - gibleed_all [416ms]
i Generating cohort (2/5) - gibleed_default
v Generating cohort (2/5) - gibleed_default [420ms]
i Generating cohort (3/5) - gibleed_default_with_descendants
v Generating cohort (3/5) - gibleed_default_with_descendants [389ms]
i Generating cohort (4/5) - gibleed_all_end_10
v Generating cohort (4/5) - gibleed_all_end_10 [409ms]
i Generating cohort (5/5) - gibleed_end_10
v Generating cohort (5/5) - gibleed_end_10 [399ms]
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [228ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [273ms]
i Generating 3 cohorts
i Generating cohort (1/3) - another_gibleed_male
v Generating cohort (1/3) - another_gibleed_male [825ms]
i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [257ms]
i Generating cohort (3/3) - another_deep_vein_thrombosis_01
v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [254ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [650ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [260ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [224ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [584ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [209ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [204ms]
i `EUNOMIA_DATA_FOLDER` set to: '/tmp/RtmpYeM9eh'.
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /tmp/RtmpYeM9eh/GiBleed_5.3.zip
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_male
v Generating cohort (1/1) - gibleed_male [698ms]
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3',
'test-04-db-generateConceptCohortSet.R:399:3',
'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:61:3',
'test-db-recordCohortAttrition.R:121:5',
'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3',
'test-write_prefix_cohort_generation_snowflake.R:4:3'
• arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'
• eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
• failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5'
• manual test (7): 'test-02-db-cdm.R:234:3',
'test-03-db-generateCohortSet.R:111:3',
'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3',
'test-Eunomia.R:2:3', 'test-db-in_schema.R:46:3',
'test-db-write_schema_with_database.R:5:3'
• {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3'
• {TreatmentPatterns} is not installed (1):
'test-03-db-generateCohortSet.R:130:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:58:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:230:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:272:3
── Failure ('test-04-db-generateConceptCohortSet.R:547:3'): invalid cdm records are ignored in generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(actual, 'cohort_codelist')` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`attr(expected, 'cohort_codelist')` is absent
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.7.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [11m/17m]
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(CDMConnector)
>
> test_check("CDMConnector")
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /tmp/RtmpqecxUD/working_dir/RtmpG0aiAj/file13cc0674381d92/GiBleed_5.3.zip
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
Support for 'prefix' in writeSchema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead.
This message is displayed once per session.
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [2.7s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [783ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [669ms]
i Generating 3 cohorts
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.6s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [567ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [666ms]
i Generating 3 cohorts
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [750ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [735ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [704ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [940ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [652ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [492ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default
v Generating cohort (1/1) - gibleed_default [1s]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default_with_descendants
v Generating cohort (1/1) - gibleed_default_with_descendants [672ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [669ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [722ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [468ms]
Attaching package: 'clock'
The following object is masked from 'package:CDMConnector':
as_date
=====>------------------------- 15% | ETA: 13s
=======================>------- 76% | ETA: 3s
==================>------------ 61% | ETA: 2s
! cdm name not specified and could not be inferred from the cdm source table
i Generating 5 cohorts
i Generating cohort (1/5) - gibleed_all
v Generating cohort (1/5) - gibleed_all [717ms]
i Generating cohort (2/5) - gibleed_default
v Generating cohort (2/5) - gibleed_default [721ms]
i Generating cohort (3/5) - gibleed_default_with_descendants
v Generating cohort (3/5) - gibleed_default_with_descendants [738ms]
i Generating cohort (4/5) - gibleed_all_end_10
v Generating cohort (4/5) - gibleed_all_end_10 [736ms]
i Generating cohort (5/5) - gibleed_end_10
v Generating cohort (5/5) - gibleed_end_10 [752ms]
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [1.1s]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [651ms]
i Generating 3 cohorts
i Generating cohort (1/3) - another_gibleed_male
v Generating cohort (1/3) - another_gibleed_male [2.1s]
i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [935ms]
i Generating cohort (3/3) - another_deep_vein_thrombosis_01
v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [536ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.8s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [1s]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [1.2s]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.6s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [837ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [730ms]
i `EUNOMIA_DATA_FOLDER` set to: '/tmp/RtmpqecxUD/working_dir/RtmpG0aiAj'.
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /tmp/RtmpqecxUD/working_dir/RtmpG0aiAj/GiBleed_5.3.zip
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_male
v Generating cohort (1/1) - gibleed_male [1.4s]
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3',
'test-04-db-generateConceptCohortSet.R:399:3',
'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:61:3',
'test-db-recordCohortAttrition.R:121:5',
'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3',
'test-write_prefix_cohort_generation_snowflake.R:4:3'
• arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'
• eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
• failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5'
• manual test (7): 'test-02-db-cdm.R:234:3',
'test-03-db-generateCohortSet.R:111:3',
'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3',
'test-Eunomia.R:2:3', 'test-db-in_schema.R:46:3',
'test-db-write_schema_with_database.R:5:3'
• {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3'
• {TreatmentPatterns} is not installed (1):
'test-03-db-generateCohortSet.R:130:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:58:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:230:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:272:3
── Failure ('test-04-db-generateConceptCohortSet.R:547:3'): invalid cdm records are ignored in generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(actual, 'cohort_codelist')` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`attr(expected, 'cohort_codelist')` is absent
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.7.0
Check: tests
Result: ERROR
Running 'testthat.R' [296s]
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(CDMConnector)
>
> test_check("CDMConnector")
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database D:\temp\2025_02_15_01_50_01_12291\RtmpAXmMj9\file9da8d0924cd/GiBleed_5.3.zip
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
Support for 'prefix' in writeSchema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead.
This message is displayed once per session.
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [771ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [233ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [263ms]
i Generating 3 cohorts
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [629ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [200ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [256ms]
i Generating 3 cohorts
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [222ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [201ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [215ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [227ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [217ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [226ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default
v Generating cohort (1/1) - gibleed_default [358ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default_with_descendants
v Generating cohort (1/1) - gibleed_default_with_descendants [343ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [283ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [336ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [205ms]
Attaching package: 'clock'
The following object is masked from 'package:CDMConnector':
as_date
! cdm name not specified and could not be inferred from the cdm source table
i Generating 5 cohorts
i Generating cohort (1/5) - gibleed_all
v Generating cohort (1/5) - gibleed_all [349ms]
i Generating cohort (2/5) - gibleed_default
v Generating cohort (2/5) - gibleed_default [335ms]
i Generating cohort (3/5) - gibleed_default_with_descendants
v Generating cohort (3/5) - gibleed_default_with_descendants [350ms]
i Generating cohort (4/5) - gibleed_all_end_10
v Generating cohort (4/5) - gibleed_all_end_10 [356ms]
i Generating cohort (5/5) - gibleed_end_10
v Generating cohort (5/5) - gibleed_end_10 [371ms]
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [243ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [215ms]
i Generating 3 cohorts
i Generating cohort (1/3) - another_gibleed_male
v Generating cohort (1/3) - another_gibleed_male [603ms]
i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [202ms]
i Generating cohort (3/3) - another_deep_vein_thrombosis_01
v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [215ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [565ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [213ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [221ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [616ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [221ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [233ms]
i `EUNOMIA_DATA_FOLDER` set to: 'D:\temp\2025_02_15_01_50_01_12291\RtmpAXmMj9'.
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database D:\temp\2025_02_15_01_50_01_12291\RtmpAXmMj9/GiBleed_5.3.zip
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_male
v Generating cohort (1/1) - gibleed_male [598ms]
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3',
'test-04-db-generateConceptCohortSet.R:399:3',
'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:61:3',
'test-db-recordCohortAttrition.R:121:5',
'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3',
'test-write_prefix_cohort_generation_snowflake.R:4:3'
• arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'
• eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
• failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5'
• manual test (7): 'test-02-db-cdm.R:234:3',
'test-03-db-generateCohortSet.R:111:3',
'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3',
'test-Eunomia.R:2:3', 'test-db-in_schema.R:46:3',
'test-db-write_schema_with_database.R:5:3'
• {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3'
• {TreatmentPatterns} is not installed (1):
'test-03-db-generateCohortSet.R:130:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:58:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:230:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:272:3
── Failure ('test-04-db-generateConceptCohortSet.R:547:3'): invalid cdm records are ignored in generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(actual, 'cohort_codelist')` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`attr(expected, 'cohort_codelist')` is absent
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.7.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [387s/586s]
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(CDMConnector)
>
> test_check("CDMConnector")
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /home/hornik/tmp/scratch/RtmpqR3bQB/file2e234713d93558/GiBleed_5.3.zip
==================>------------ 61% | ETA: 2s
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
Support for 'prefix' in writeSchema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead.
This message is displayed once per session.
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.6s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [416ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [451ms]
i Generating 3 cohorts
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.2s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [590ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [392ms]
i Generating 3 cohorts
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [433ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [401ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [433ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [293ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [483ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [520ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default
v Generating cohort (1/1) - gibleed_default [573ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default_with_descendants
v Generating cohort (1/1) - gibleed_default_with_descendants [646ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [543ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [624ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [438ms]
Attaching package: 'clock'
The following object is masked from 'package:CDMConnector':
as_date
================>-------------- 55% | ETA: 3s
=====================>--------- 70% | ETA: 1s
! cdm name not specified and could not be inferred from the cdm source table
i Generating 5 cohorts
i Generating cohort (1/5) - gibleed_all
v Generating cohort (1/5) - gibleed_all [575ms]
i Generating cohort (2/5) - gibleed_default
v Generating cohort (2/5) - gibleed_default [868ms]
i Generating cohort (3/5) - gibleed_default_with_descendants
v Generating cohort (3/5) - gibleed_default_with_descendants [573ms]
i Generating cohort (4/5) - gibleed_all_end_10
v Generating cohort (4/5) - gibleed_all_end_10 [582ms]
i Generating cohort (5/5) - gibleed_end_10
v Generating cohort (5/5) - gibleed_end_10 [518ms]
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [464ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [429ms]
i Generating 3 cohorts
i Generating cohort (1/3) - another_gibleed_male
v Generating cohort (1/3) - another_gibleed_male [1.3s]
i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [463ms]
i Generating cohort (3/3) - another_deep_vein_thrombosis_01
v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [499ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.5s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [257ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [278ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.1s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [430ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [494ms]
i `EUNOMIA_DATA_FOLDER` set to: '/home/hornik/tmp/scratch/RtmpqR3bQB'.
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /home/hornik/tmp/scratch/RtmpqR3bQB/GiBleed_5.3.zip
=========================>----- 83% | ETA: 1s
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_male
v Generating cohort (1/1) - gibleed_male [1.2s]
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3',
'test-04-db-generateConceptCohortSet.R:399:3',
'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:61:3',
'test-db-recordCohortAttrition.R:121:5',
'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3',
'test-write_prefix_cohort_generation_snowflake.R:4:3'
• arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'
• eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
• failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5'
• manual test (7): 'test-02-db-cdm.R:234:3',
'test-03-db-generateCohortSet.R:111:3',
'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3',
'test-Eunomia.R:2:3', 'test-db-in_schema.R:46:3',
'test-db-write_schema_with_database.R:5:3'
• {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3'
• {TreatmentPatterns} is not installed (1):
'test-03-db-generateCohortSet.R:130:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:58:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:230:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:272:3
── Failure ('test-04-db-generateConceptCohortSet.R:547:3'): invalid cdm records are ignored in generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(actual, 'cohort_codelist')` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`attr(expected, 'cohort_codelist')` is absent
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.7.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [392s/595s]
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(CDMConnector)
>
> test_check("CDMConnector")
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /home/hornik/tmp/scratch/RtmpXuONbD/file2bd4fa15383472/GiBleed_5.3.zip
=====================>--------- 71% | ETA: 1s
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
Support for 'prefix' in writeSchema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead.
This message is displayed once per session.
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.7s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [402ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [441ms]
i Generating 3 cohorts
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.4s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [486ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [449ms]
i Generating 3 cohorts
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [526ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [503ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [414ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [441ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [512ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [424ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 2 cohorts
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default
v Generating cohort (1/1) - gibleed_default [730ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_default_with_descendants
v Generating cohort (1/1) - gibleed_default_with_descendants [628ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [656ms]
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_all
v Generating cohort (1/1) - gibleed_all [443ms]
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [466ms]
Attaching package: 'clock'
The following object is masked from 'package:CDMConnector':
as_date
==============>---------------- 45% | ETA: 4s
=================>------------- 58% | ETA: 2s
! cdm name not specified and could not be inferred from the cdm source table
i Generating 5 cohorts
i Generating cohort (1/5) - gibleed_all
v Generating cohort (1/5) - gibleed_all [512ms]
i Generating cohort (2/5) - gibleed_default
v Generating cohort (2/5) - gibleed_default [689ms]
i Generating cohort (3/5) - gibleed_default_with_descendants
v Generating cohort (3/5) - gibleed_default_with_descendants [705ms]
i Generating cohort (4/5) - gibleed_all_end_10
v Generating cohort (4/5) - gibleed_all_end_10 [693ms]
i Generating cohort (5/5) - gibleed_end_10
v Generating cohort (5/5) - gibleed_end_10 [707ms]
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [456ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01
v Generating cohort (2/2) - deep_vein_thrombosis_01 [517ms]
i Generating 3 cohorts
i Generating cohort (1/3) - another_gibleed_male
v Generating cohort (1/3) - another_gibleed_male [1.3s]
i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [401ms]
i Generating cohort (3/3) - another_deep_vein_thrombosis_01
v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [579ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [409ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [399ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male
v Generating cohort (1/3) - gibleed_male [1.4s]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [367ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01
v Generating cohort (3/3) - deep_vein_thrombosis_01 [504ms]
i `EUNOMIA_DATA_FOLDER` set to: '/home/hornik/tmp/scratch/RtmpXuONbD'.
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Download completed!
Creating CDM database /home/hornik/tmp/scratch/RtmpXuONbD/GiBleed_5.3.zip
============>------------------ 41% | ETA: 3s
Getting distinct count of concept relationship table
Getting count of different relationship IDs in concept relationship table
Getting join of concept and concept class computed to a temp table
Getting concept table collected into memory
Getting join of person and observation period collected into memory
Getting summary of observation period start and end dates by gender concept id
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
i Generating 1 cohort
i Generating cohort (1/1) - gibleed_male
v Generating cohort (1/1) - gibleed_male [1.1s]
Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
target signature 'duckdb_connection#Id'.
"duckdb_connection#ANY" would also be valid
! cdm name not specified and could not be inferred from the cdm source table
! cdm name not specified and could not be inferred from the cdm source table
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3',
'test-04-db-generateConceptCohortSet.R:399:3',
'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:61:3',
'test-db-recordCohortAttrition.R:121:5',
'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3',
'test-write_prefix_cohort_generation_snowflake.R:4:3'
• arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'
• eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
• failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5'
• manual test (7): 'test-02-db-cdm.R:234:3',
'test-03-db-generateCohortSet.R:111:3',
'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3',
'test-Eunomia.R:2:3', 'test-db-in_schema.R:46:3',
'test-db-write_schema_with_database.R:5:3'
• {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3'
• {TreatmentPatterns} is not installed (1):
'test-03-db-generateCohortSet.R:130:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:58:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:230:3
── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1
`attr(attr(expected, 'cohort_codelist'), 'row.names')`:
`attr(actual, 'cohort_codelist')$cohort_definition_id`: 1
`attr(expected, 'cohort_codelist')$cohort_definition_id`:
`attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"
`attr(expected, 'cohort_codelist')$codelist_name`:
`attr(actual, 'cohort_codelist')$concept_id`: 192671
`attr(expected, 'cohort_codelist')$concept_id`:
`attr(actual, 'cohort_codelist')$type`: "index event"
`attr(expected, 'cohort_codelist')$type`:
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5
2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:272:3
── Failure ('test-04-db-generateConceptCohortSet.R:547:3'): invalid cdm records are ignored in generateConceptCohortSet ──
`actual` (`actual`) not equal to `expected` (`expected`).
`attr(actual, 'cohort_codelist')` is an S3 object of class <tbl_df/tbl/data.frame>, a list
`attr(expected, 'cohort_codelist')` is absent
[ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.