Last updated on 2026-02-16 19:50:54 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.0 | 12.34 | 378.98 | 391.32 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.0 | 8.42 | 277.30 | 285.72 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.5.0 | 19.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.5.0 | 20.00 | 466.67 | 486.67 | ERROR | |
| r-devel-macos-arm64 | 0.5.0 | 3.00 | 690.00 | 693.00 | OK | |
| r-devel-windows-x86_64 | 0.5.0 | 14.00 | 561.00 | 575.00 | OK | |
| r-patched-linux-x86_64 | 0.5.0 | 11.36 | 352.79 | 364.15 | OK | |
| r-release-linux-x86_64 | 0.5.0 | 10.47 | 353.95 | 364.42 | OK | |
| r-release-macos-arm64 | 0.5.0 | 3.00 | 1033.00 | 1036.00 | OK | |
| r-release-macos-x86_64 | 0.5.0 | 8.00 | 771.00 | 779.00 | OK | |
| r-release-windows-x86_64 | 0.5.0 | 14.00 | 534.00 | 548.00 | OK | |
| r-oldrel-macos-arm64 | 0.5.0 | 3.00 | 1474.00 | 1477.00 | OK | |
| r-oldrel-macos-x86_64 | 0.5.0 | 15.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.5.0 | 17.00 | 706.00 | 723.00 | OK |
Version: 0.5.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [326s/420s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(TestGenerator)
>
> test_check("TestGenerator")
v All tables are valid
v All tables are valid
v All tables are valid. Non-standard table(s) in test data: pregnancy
x The following tables are invalid: pregnancy
v All tables are valid
v Unit Test Definition Created Successfully: 'test'
v All tables are valid. Non-standard table(s) in test data: pregnancy
v Unit Test Definition Created Successfully: 'pregnancy'
v All tables are valid
v Unit Test Definition Created Successfully: 'test'
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/empty_cdm_5.3.zip'
Content type 'application/zip' length 821216248 bytes (783.2 MB)
==================================================
downloaded 783.2 MB
Download completed!
Creating CDM database /tmp/RtmpBsp5z9/working_dir/RtmpzIpLhQ/empty_cdm_5.3.zip
===================>----------- 63% | ETA: 6s
=======================>------- 78% | ETA: 6s
========================>------ 80% | ETA: 6s
! cdm name not specified and could not be inferred from the cdm source table
x Non-standard table(s) in test data: pregnancy
x Standard table(s) in test data: person, observation_period, condition_occurrence, measurement, drug_exposure, visit_detail, visit_occurrence, procedure_occurrence, device_exposure, observation, note, death, note_nlp, specimen and fact_relationship
v Patients pushed to blank CDM successfully
v All tables are valid. Non-standard table(s) in test data: pregnancy
v Unit Test Definition Created Successfully: 'pregnancy'
! cdm name not specified and could not be inferred from the cdm source table
x Non-standard table(s) in test data: pregnancy
x Standard table(s) in test data: person, observation_period, condition_occurrence, measurement, drug_exposure, visit_detail, visit_occurrence, procedure_occurrence, device_exposure, observation, note, death, note_nlp, specimen and fact_relationship
v Patients pushed to blank CDM successfully
v All tables are valid
v Unit Test Definition Created Successfully: 'test'
! cdm name not specified and could not be inferred from the cdm source table
x Standard table(s) in test data: person, observation_period, condition_occurrence, measurement, drug_exposure, visit_detail, visit_occurrence, procedure_occurrence, device_exposure, observation, death, note, note_nlp, specimen and fact_relationship
v Patients pushed to blank CDM successfully
v All tables are valid
v Unit Test Definition Created Successfully: 'test'
! cdm name not specified and could not be inferred from the cdm source table
x Standard table(s) in test data: person, observation_period, condition_occurrence, measurement, drug_exposure, visit_detail, visit_occurrence, procedure_occurrence, device_exposure, observation, death, note, note_nlp, specimen and fact_relationship
v Patients pushed to blank CDM successfully
v Unit Test Definition Created Successfully: 'mimic_sample'
trying URL 'https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip'
Content type 'application/zip' length 10786504 bytes (10.3 MB)
==================================================
downloaded 10.3 MB
! Empty Tables Found:
attribute_definition, cohort_definition, cost, metadata, note, note_nlp,
payer_plan_period, provider
v Unit Test Definition Created Successfully: 'test'
trying URL 'https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip'
Saving _problems/test-patients-172.R
Bad Gateway (HTTP 502).v All tables are valid. Non-standard table(s) in test data: pregnancy
v Unit Test Definition Created Successfully: 'pregnancy'
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/empty_cdm_5.4.zip'
Content type 'application/zip' length 772029174 bytes (736.3 MB)
==================================================
downloaded 736.3 MB
Download completed!
Creating CDM database /tmp/RtmpBsp5z9/working_dir/RtmpzIpLhQ/empty_cdm_5.4.zip
====================>---------- 65% | ETA: 5s
========================>------ 79% | ETA: 5s
========================>------ 81% | ETA: 5s
==========================>---- 86% | ETA: 4s
! cdm name not specified and could not be inferred from the cdm source table
x Non-standard table(s) in test data: pregnancy
x Standard table(s) in test data: person, observation_period, condition_occurrence, measurement, drug_exposure, visit_detail, visit_occurrence, procedure_occurrence, device_exposure, observation, note, death, note_nlp, specimen and fact_relationship
v Patients pushed to blank CDM successfully
[ FAIL 1 | WARN 6 | SKIP 2 | PASS 33 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-patients.R:197:1'
• manual test (1): 'test-utilsCdm.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-patients.R:169:3'): Mimic data Patients to CDM function ────────
Error in `utils::download.file(url = remoteResource, destfile = file.path(pathToData, zipName), mode = "wb", method = "auto", quiet = FALSE, extra = list(progressfunction = function(downloaded, total) { progress <- min(1, downloaded/total) cli::cli_progress_update(id = pb, set = progress) }))`: cannot open URL 'https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip'
Backtrace:
▆
1. └─TestGenerator::downloadTestData(...) at test-patients.R:169:3
2. ├─withr::with_options(...)
3. │ └─base::force(code)
4. └─utils::download.file(...)
[ FAIL 1 | WARN 6 | SKIP 2 | PASS 33 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘arrow’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64