* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/PatientProfiles.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 07:59:09 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘PatientProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PatientProfiles’ version ‘1.6.1’
* 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 ‘PatientProfiles’ 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 ... [12s/15s] 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 R/sysdata.rda ... 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 ‘spelling.R’
  Running ‘testthat.R’ [15s/14s]
 [16s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s/16s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown

Quitting from cohort-intersect.Rmd:22-36 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'duckdb'
---
Backtrace:
    ▆
 1. ├─PatientProfiles::mockPatientProfiles(...)
 2. │ └─CDMConnector::dbSource(...)
 3. │   └─methods::is(con, "Pool")
 4. └─base::loadNamespace(x)
 5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 6.     └─base (local) withOneRestart(expr, restarts[[1L]])
 7.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘cohort-intersect.Rmd’

--- re-building ‘demographics.rmd’ using rmarkdown

Quitting from demographics.rmd:19-28 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'duckdb'
---
Backtrace:
    ▆
 1. └─base::library(duckdb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'demographics.rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘demographics.rmd’

--- re-building ‘event.rmd’ using rmarkdown

Quitting from event.rmd:47-55 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockCdmFromDataset()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'event.rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘event.rmd’

SUMMARY: processing the following files failed:
  ‘cohort-intersect.Rmd’ ‘demographics.rmd’ ‘event.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: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-clang-trunk/PatientProfiles.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:36.33, 74.08 + 7.18