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Last updated on 2026-09-21 17:51:25 CEST.
| Package | OK | ERROR |
|---|---|---|
| MeasurementDiagnostics | 12 | 1 |
| visOmopResults | 13 |
Current CRAN status: OK: 12, ERROR: 1
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MeasurementDiagnostics)
>
> test_check("MeasurementDiagnostics")
Saving _problems/test-plotMeasurementValueAsConcept-3.R
Saving _problems/test-plotMeasurementValueAsNumeric-3.R
Saving _problems/test-tableMeasurementSummary-3.R
Saving _problems/test-tableMeasurementValueAsConcept-3.R
Saving _problems/test-tableMeasurementValueAsNumeric-3.R
[ FAIL 5 | WARN 0 | SKIP 10 | PASS 0 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotMeasurementSummary.R:2:3',
'test-summariseCohortMeasurementUse.R:2:3',
'test-summariseCohortMeasurementUse.R:176:3',
'test-summariseCohortMeasurementUse.R:282:3',
'test-summariseCohortMeasurementUse.R:353:3',
'test-summariseMeasurementUse.R:2:3', 'test-summariseMeasurementUse.R:211:3',
'test-summariseMeasurementUse.R:276:3',
'test-summariseMeasurementUse.R:447:3',
'test-summariseMeasurementUse.R:491:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotMeasurementValueAsConcept.R:3:3'): plotMeasurementValueAsConcept works ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─MeasurementDiagnostics:::copyCdm(cdm) at test-plotMeasurementValueAsConcept.R:3:3
2. │ ├─CDMConnector::dbSource(con = connection(), writeSchema = writeSchema()) at ./setup.R:36:5
3. │ │ └─methods::is(con, "Pool")
4. │ └─MeasurementDiagnostics:::connection()
5. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./setup.R:12:3
6. ├─base::loadNamespace(x)
7. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
9. │ │ └─base (local) doWithOneRestart(return(expr), restart)
10. │ └─base::stop(cond)
11. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-plotMeasurementValueAsNumeric.R:3:3'): plotMeasurementValueAsNumber works ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─MeasurementDiagnostics:::copyCdm(cdm) at test-plotMeasurementValueAsNumeric.R:3:3
2. │ ├─CDMConnector::dbSource(con = connection(), writeSchema = writeSchema()) at ./setup.R:36:5
3. │ │ └─methods::is(con, "Pool")
4. │ └─MeasurementDiagnostics:::connection()
5. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./setup.R:12:3
6. ├─base::loadNamespace(x)
7. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
9. │ │ └─base (local) doWithOneRestart(return(expr), restart)
10. │ └─base::stop(cond)
11. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-tableMeasurementSummary.R:3:3'): check that it works ──────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─MeasurementDiagnostics:::copyCdm(cdm) at test-tableMeasurementSummary.R:3:3
2. │ ├─CDMConnector::dbSource(con = connection(), writeSchema = writeSchema()) at ./setup.R:36:5
3. │ │ └─methods::is(con, "Pool")
4. │ └─MeasurementDiagnostics:::connection()
5. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./setup.R:12:3
6. ├─base::loadNamespace(x)
7. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
9. │ │ └─base (local) doWithOneRestart(return(expr), restart)
10. │ └─base::stop(cond)
11. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-tableMeasurementValueAsConcept.R:3:3'): table works ────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─MeasurementDiagnostics:::copyCdm(cdm) at test-tableMeasurementValueAsConcept.R:3:3
2. │ ├─CDMConnector::dbSource(con = connection(), writeSchema = writeSchema()) at ./setup.R:36:5
3. │ │ └─methods::is(con, "Pool")
4. │ └─MeasurementDiagnostics:::connection()
5. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./setup.R:12:3
6. ├─base::loadNamespace(x)
7. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
9. │ │ └─base (local) doWithOneRestart(return(expr), restart)
10. │ └─base::stop(cond)
11. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-tableMeasurementValueAsNumeric.R:3:3'): table works ────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─MeasurementDiagnostics:::copyCdm(cdm) at test-tableMeasurementValueAsNumeric.R:3:3
2. │ ├─CDMConnector::dbSource(con = connection(), writeSchema = writeSchema()) at ./setup.R:36:5
3. │ │ └─methods::is(con, "Pool")
4. │ └─MeasurementDiagnostics:::connection()
5. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./setup.R:12:3
6. ├─base::loadNamespace(x)
7. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
9. │ │ └─base (local) doWithOneRestart(return(expr), restart)
10. │ └─base::stop(cond)
11. └─base (local) `<fn>`(`<pckgNtFE>`)
[ FAIL 5 | WARN 0 | SKIP 10 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_summariseMeasurementUse.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from a01_summariseMeasurementUse.Rmd:28-33 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'duckdb'
---
Backtrace:
▆
1. └─base::library(duckdb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a01_summariseMeasurementUse.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘a01_summariseMeasurementUse.Rmd’
--- re-building ‘a02_summariseCohortMeasurementUse.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from a02_summariseCohortMeasurementUse.Rmd:30-38 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
---
Backtrace:
▆
1. ├─MeasurementDiagnostics::mockMeasurementDiagnostics()
2. │ ├─CDMConnector::copyCdmTo(...)
3. │ │ ├─checkmate::assertTRUE(DBI::dbIsValid(con))
4. │ │ │ └─checkmate::checkTRUE(x, na.ok)
5. │ │ │ └─base::isTRUE(x)
6. │ │ └─DBI::dbIsValid(con)
7. │ └─DBI::dbConnect(duckdb::duckdb())
8. ├─base::loadNamespace(x)
9. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
11. │ │ └─base (local) doWithOneRestart(return(expr), restart)
12. │ └─base::stop(cond)
13. ├─base (local) `<fn>`(`<pckgNtFE>`)
14. └─base::.handleSimpleError(...)
15. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a02_summariseCohortMeasurementUse.Rmd' failed with diagnostics:
error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
--- failed re-building ‘a02_summariseCohortMeasurementUse.Rmd’
--- re-building ‘a03_resultsVisualisation.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from a03_resultsVisualisation.Rmd:28-38 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
---
Backtrace:
▆
1. ├─MeasurementDiagnostics::mockMeasurementDiagnostics()
2. │ ├─CDMConnector::copyCdmTo(...)
3. │ │ ├─checkmate::assertTRUE(DBI::dbIsValid(con))
4. │ │ │ └─checkmate::checkTRUE(x, na.ok)
5. │ │ │ └─base::isTRUE(x)
6. │ │ └─DBI::dbIsValid(con)
7. │ └─DBI::dbConnect(duckdb::duckdb())
8. ├─base::loadNamespace(x)
9. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
11. │ │ └─base (local) doWithOneRestart(return(expr), restart)
12. │ └─base::stop(cond)
13. ├─base (local) `<fn>`(`<pckgNtFE>`)
14. └─base::.handleSimpleError(...)
15. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a03_resultsVisualisation.Rmd' failed with diagnostics:
error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
--- failed re-building ‘a03_resultsVisualisation.Rmd’
SUMMARY: processing the following files failed:
‘a01_summariseMeasurementUse.Rmd’
‘a02_summariseCohortMeasurementUse.Rmd’
‘a03_resultsVisualisation.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 13
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