Last updated on 2024-04-23 10:54:31 CEST.
Package | ERROR | NOTE |
---|---|---|
CDMConnector | 1 | 13 |
Current CRAN status: ERROR: 1, NOTE: 13
Version: 1.3.1
Check: package dependencies
Result: NOTE
Package which this enhances but not available for checking: ‘Capr’
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-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [284s/276s]
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/Rtmpo0Da3I/working_dir/Rtmp19R0zo/file3031ae1bf81ec3/GiBleed_5.3.zip
====================>---------- 67% | ETA: 1s
i Generating 5 cohorts
i Generating cohort (1/5) - gibleed_all)
v Generating cohort (1/5) - gibleed_all) [761ms]
i Generating cohort (2/5) - gibleed_all_end_10)
v Generating cohort (2/5) - gibleed_all_end_10) [513ms]
i Generating cohort (3/5) - gibleed_default)
v Generating cohort (3/5) - gibleed_default) [335ms]
i Generating cohort (4/5) - gibleed_default_with_descendants)
v Generating cohort (4/5) - gibleed_default_with_descendants) [340ms]
i Generating cohort (5/5) - gibleed_end_10)
v Generating cohort (5/5) - gibleed_end_10) [359ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male)
v Generating cohort (1/3) - gibleed_male) [822ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [230ms]
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 3 cohorts
i Generating cohort (1/3) - gibleed_male)
v Generating cohort (1/3) - gibleed_male) [743ms]
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) [273ms]
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) [253ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01)
v Generating cohort (2/2) - deep_vein_thrombosis_01) [334ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [231ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01)
v Generating cohort (2/2) - deep_vein_thrombosis_01) [215ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [208ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01)
v Generating cohort (2/2) - deep_vein_thrombosis_01) [264ms]
i Generating 2 cohorts
i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [267ms]
i Generating cohort (2/2) - deep_vein_thrombosis_01)
v Generating cohort (2/2) - deep_vein_thrombosis_01) [287ms]
i Generating 3 cohorts
i Generating cohort (1/3) - another_gibleed_male)
v Generating cohort (1/3) - another_gibleed_male) [916ms]
i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01)
v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01) [319ms]
i Generating cohort (3/3) - another_deep_vein_thrombosis_01)
v Generating cohort (3/3) - another_deep_vein_thrombosis_01) [308ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male)
v Generating cohort (1/3) - gibleed_male) [635ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [249ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01)
v Generating cohort (3/3) - deep_vein_thrombosis_01) [286ms]
i Generating 3 cohorts
i Generating cohort (1/3) - gibleed_male)
v Generating cohort (1/3) - gibleed_male) [571ms]
i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [232ms]
i Generating cohort (3/3) - deep_vein_thrombosis_01)
v Generating cohort (3/3) - deep_vein_thrombosis_01) [270ms]
[ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• Capr cannot be loaded (1): 'test-db-generateCohortSet.R:77:3'
• On CRAN (9): 'test-db-generateCohortSet.R:128:3',
'test-db-generateConceptCohortSet.R:315:3',
'test-db-generateConceptCohortSet.R:332:3',
'test-db-generateConceptCohortSet.R:357:3',
'test-db-recordCohortAttrition.R:121:5',
'test-db-recordCohortAttrition.R:134:3', 'test-local_cdm.R:5:3',
'test-memory-issue.R:6:3',
'test-write_prefix_cohort_generation_snowflake.R:4:3'
• eunomia_is_available("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
• failing test (1): 'test-db-dateadd.R:126:3'
• manual test (5): 'test-Eunomia.R:2:3', 'test-db-copy_cdm_to.R:62:3',
'test-db-generateCohortSet.R:108:3', 'test-db-generateCohortSet.R:243:3',
'test-db-write_schema_with_database.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-db-generateConceptCohortSet.R:308:5'): duckdb - generateConceptCohortSet ──
Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
Backtrace:
▆
1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-db-generateConceptCohortSet.R:308:5
2. └─CDMConnector::generateConceptCohortSet(...) at test-db-generateConceptCohortSet.R:18:3
3. └─base::Ops.numeric_version(...)
4. └─base::as.numeric_version(e2)
5. └─base::numeric_version(x)
6. └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
[ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ]
Error: Test failures
In addition: Warning message:
Connection is garbage-collected, use dbDisconnect() to avoid this.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3.1
Check: package dependencies
Result: NOTE
Packages which this enhances but not available for checking:
'CirceR', 'Capr'
Flavors: r-prerel-macos-arm64, r-prerel-macos-x86_64, r-prerel-windows-x86_64, r-patched-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64