* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/MeasurementDiagnostics.Rcheck’
* using R Under development (unstable) (2026-09-03 r90476)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 23.1.0
    flang version 23.1.0
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-09-03 07:59:08 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘MeasurementDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MeasurementDiagnostics’ version ‘0.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘duckdb’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MeasurementDiagnostics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/18s] 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

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs
See
  ‘/data/localhost/ripley/R/packages/tests-clang-trunk/MeasurementDiagnostics.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 0:57.90, 40.27 + 5.33