Last updated on 2024-04-18 12:52:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.4 | 5.96 | 377.42 | 383.38 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4 | 4.28 | 260.43 | 264.71 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4 | 436.29 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.4 | 432.83 | OK | |||
| r-prerel-macos-arm64 | 1.0.4 | 134.00 | OK | |||
| r-prerel-macos-x86_64 | 1.0.4 | 406.00 | OK | |||
| r-prerel-windows-x86_64 | 1.0.4 | 6.00 | 152.00 | 158.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.4 | 3.33 | 358.76 | 362.09 | OK | |
| r-release-linux-x86_64 | 1.0.4 | 3.29 | 359.48 | 362.77 | OK | |
| r-release-macos-arm64 | 1.0.4 | 125.00 | OK | |||
| r-release-macos-x86_64 | 1.0.4 | 380.00 | OK | |||
| r-release-windows-x86_64 | 1.0.4 | 7.00 | 328.00 | 335.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.4 | 113.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.4 | 7.00 | 327.00 | 334.00 | OK |
Version: 1.0.4
Check: tests
Result: ERROR
Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(DrugExposureDiagnostics)
>
> test_check("DrugExposureDiagnostics")
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Joining with `by = join_by(ingredient_concept_id)`
Joining with `by = join_by(ingredient_concept_id)`
Joining with `by = join_by(ingredient_concept_id)`
Time taken: 0 minutes and 0 seconds
testMessage
[ FAIL 11 | WARN 29 | SKIP 1 | PASS 250 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• Sys.getenv("TESTDB_USER") == "" is TRUE (1): 'test-SyntheaSqlServer.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Eunomia.R:3:3'): execute default checks, default ingredient, verbose ──
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm() at test-Eunomia.R:3:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:23:3'): execute all checks, given ingredient ─────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:23:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:39:3'): execute some checks, given ingredient ────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:39:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:54:3'): execute all checks: expected errors ──────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:54:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:65:3'): each check ───────────────────────────────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:65:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:103:3'): each check: expected errors ─────────────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:103:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:128:3'): get number of Days_supply that are incorrect ──
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:128:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:144:3'): sampling ────────────────────────────────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:144:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:164:3'): summary ─────────────────────────────────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:164:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:182:3'): subset on specific concepts ─────────────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:182:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
── Error ('test-Eunomia.R:227:3'): obscuring results by minCellCount ───────────
Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.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://example-data.ohdsi.dev/GiBleed.zip'
Backtrace:
▆
1. └─DrugExposureDiagnostics::getEunomiaCdm(1125315) at test-Eunomia.R:227:3
2. ├─utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER")))
3. │ └─base::withVisible(...elt(i))
4. └─CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))
5. ├─withr::with_options(...)
6. │ └─base::force(code)
7. └─utils::download.file(...)
[ FAIL 11 | WARN 29 | SKIP 1 | PASS 250 ]
Error: Test failures
Execution halted
Flavor: r-prerel-windows-x86_64
Version: 1.0.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'IntroductionToDrugExposureDiagnostics.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Quitting from lines at lines 26-27 [unnamed-chunk-2] (IntroductionToDrugExposureDiagnostics.Rmd)
Error: processing vignette 'IntroductionToDrugExposureDiagnostics.Rmd' failed with diagnostics:
cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip'
--- failed re-building 'IntroductionToDrugExposureDiagnostics.Rmd'
--- re-building 'SummaryOfChecks.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Quitting from lines at lines 22-32 [setup] (SummaryOfChecks.Rmd)
Error: processing vignette 'SummaryOfChecks.Rmd' failed with diagnostics:
cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip'
--- failed re-building 'SummaryOfChecks.Rmd'
SUMMARY: processing the following files failed:
'IntroductionToDrugExposureDiagnostics.Rmd' 'SummaryOfChecks.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-prerel-windows-x86_64