• using R version 4.6.0 (2026-04-24)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22]     GNU Fortran (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22]
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-05-16 08:04:00 UTC
• 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 See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] 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 ... [7s/9s] OK
• checking Rd files ... [0s/0s] 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 ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/10s] ERROR   Running ‘testthat.R’ [8s/10s] 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 ... [17s/24s] 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 ... [4s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs