* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/OmopSketch.Rcheck’
* using R Under development (unstable) (2026-06-19 r90178)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-06-19 10:42:06 UTC
* checking for file ‘OmopSketch/DESCRIPTION’ ... OK
* this is package ‘OmopSketch’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘OmopSketch’ can be installed ... 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 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 ... [10s/10s] 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 examples with --run-donttest ... [12s/12s] ERROR
Running examples in ‘OmopSketch-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotConceptSetCounts
> ### Title: Plot the concept counts of a summariseConceptSetCounts output
> ### Aliases: plotConceptSetCounts
> 
> ### ** Examples
> 
> ## No test: 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(OmopSketch)
> library(omock)
> 
> cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
ℹ Loading bundled GiBleed tables from package data.
ℹ Adding drug_strength table.
ℹ Creating local <cdm_reference> object.
ℹ Inserting <cdm_reference> into duckdb.
> 
> result <- summariseConceptSetCounts(
+   cdm = cdm,
+   conceptSet = list(
+     "asthma" = c(4051466, 317009),
+     "rhinitis" = c(4280726, 4048171, 40486433)
+   )
+ )
Warning: `summariseConceptSetCounts()` was deprecated in OmopSketch 0.5.0.
Warning: ! `codelist` cast to integers.
ℹ Searching concepts from domain condition in condition_occurrence.
Error in `dbSendQuery()`:
! Binder Error: Referenced column "index_date" not found in FROM clause!
Candidate bindings: "condition_end_date", "condition_end_datetime", "provider_id", "condition_start_datetime", "period_type_concept_id"

LINE 18:   WHERE (index_date >= observation_period.observation_period_start_date...
                  ^
ℹ Context: rapi_prepare
ℹ Error type: BINDER
Backtrace:
     ▆
  1. ├─OmopSketch::summariseConceptSetCounts(...)
  2. │ ├─dplyr::compute(...)
  3. │ └─omopgenerics:::compute.cdm_table(...)
  4. │   ├─dplyr::compute(...)
  5. │   └─CDMConnector:::compute.db_cdm(...)
  6. │     └─CDMConnector:::.computeQuery(...)
  7. │       └─CDMConnector:::.computePermanent(...)
  8. │         ├─DBI::dbExecute(x$src$con, sql)
  9. │         └─DBI::dbExecute(x$src$con, sql)
 10. │           ├─DBI::dbSendStatement(conn, statement, ...)
 11. │           └─DBI::dbSendStatement(conn, statement, ...)
 12. │             ├─DBI::dbSendQuery(conn, statement, ...)
 13. │             └─duckdb::dbSendQuery(conn, statement, ...)
 14. │               └─duckdb (local) .local(conn, statement, ...)
 15. │                 └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
 16. │                   ├─rlang::try_fetch(...)
 17. │                   │ ├─base::tryCatch(...)
 18. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 19. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 21. │                   │ └─base::withCallingHandlers(...)
 22. │                   └─duckdb:::rapi_prepare(conn, query, env)
 23. ├─duckdb (local) `<fn>`(...)
 24. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
 25. │   └─rlang:::signal_abort(cnd, .file)
 26. │     └─base::signalCondition(cnd)
 27. └─rlang (local) `<fn>`(`<dckdb_rr>`)
 28.   └─handlers[[1L]](cnd)
 29.     └─duckdb:::rethrow_error_from_rapi(e, call)
 30.       └─rlang::abort(msg, call = call)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [235s/199s]
 [235s/199s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [23s/23s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/OmopSketch.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:47.09, 305.82 + 16.38