Last updated on 2025-02-11 07:48:46 CET.
| Package | ERROR | OK |
|---|---|---|
| TestGenerator | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 0.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [172s/341s]
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 Unit Test Definition Created Successfully: 'test'
v Unit Test Definition Created Successfully: 'test'
trying URL 'https://example-data.ohdsi.dev/empty_cdm.zip'
Content type 'application/zip' length 821216248 bytes (783.2 MB)
==================================================
downloaded 783.2 MB
Download completed!
Creating CDM database /home/hornik/tmp/scratch/Rtmp24jmc3/empty_cdm_5.3.zip
===================>----------- 63% | ETA: 4s
========================>------ 80% | ETA: 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
v Patients pushed to blank CDM successfully
v Unit Test Definition Created Successfully: 'test'
! cdm name not specified and could not be inferred from the cdm source table
v Patients pushed to blank CDM successfully
v Unit Test Definition Created Successfully: 'test'
! cdm name not specified and could not be inferred from the cdm source table
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
Download completed!
! 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'
Content type 'application/zip' length 10786504 bytes (10.3 MB)
==================================================
downloaded 10.3 MB
Download completed!
! Empty Tables Found:
attribute_definition, cohort_definition, cost, metadata, note, note_nlp,
payer_plan_period, provider
! Table with non unique ids and filled with num seq:
measurement, observation
v IDs successfully reduced
v Unit Test Definition Created Successfully: 'test'
v Patients pushed to blank CDM successfully
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'
[ FAIL 1 | WARN 22 | SKIP 1 | PASS 21 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• manual test (1): 'test-utilsCdm.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-patients.R:118:3'): convert ids function ───────────────────────
Error in `utils::download.file(url = "https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip",
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:118:3
2. ├─withr::with_options(...)
3. │ └─base::force(code)
4. └─utils::download.file(...)
[ FAIL 1 | WARN 22 | SKIP 1 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64