* using log directory 'd:/Rcompile/CRANpkg/local/4.6/shinyCohortBuilder.Rcheck'
* using R version 4.6.1 (2026-06-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-07-04 05:23:32 UTC
* checking for file 'shinyCohortBuilder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'shinyCohortBuilder' version '0.4.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'shinyCohortBuilder' 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 ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking whether startup messages can be suppressed ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: 'cohortBuilder:::get_filter_state'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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] ERROR
Running examples in 'shinyCohortBuilder-Ex.R' failed
The error most likely occurred in:

> ### Name: autofilter
> ### Title: Generate filters definition based on the Source data
> ### Aliases: autofilter autofilter.default autofilter.tblist
> 
> ### ** Examples
> 
> library(magrittr)
> library(cohortBuilder)

Attaching package: 'cohortBuilder'

The following object is masked from 'package:shinyCohortBuilder':

    autofilter

The following objects are masked from 'package:stats':

    filter, step

> library(shinyCohortBuilder)
> 
> iris_source <- set_source(tblist(iris = iris)) %>%
+   autofilter()
> iris_cohort <- cohort(iris_source)
Error in `map()`:
ℹ In index: 1.
ℹ With name: iris-SepalLength.
Caused by error:
! Can't get S7 properties with `$`. Did you mean `filter@gui`?
Backtrace:
     ▆
  1. ├─cohortBuilder::cohort(iris_source)
  2. │ └─Cohort$new(...) at cohortBuilder/R/cohort_methods.R:1297:3
  3. │   └─cohortBuilder (local) initialize(...)
  4. │     └─private$init_source(source, ...) at cohortBuilder/R/cohort_methods.R:47:9
  5. │       └─cohortBuilder:::run_hooks(hook$post, self, private, ...) at cohortBuilder/R/cohort_methods.R:1266:7
  6. │         └─shinyCohortBuilder (local) hook(...) at cohortBuilder/R/hooks.R:116:7
  7. │           └─public$modify(...)
  8. │             └─shinyCohortBuilder (local) modifier(self, private) at cohortBuilder/R/cohort_methods.R:1212:7
  9. │               └─shinyCohortBuilder:::attach_filters_gui(private$steps[[step_id]])
 10. │                 └─step$filters %>% purrr::modify(attach_filter_gui)
 11. ├─purrr::modify(., attach_filter_gui)
 12. │ └─purrr::map(vec_proxy(.x), .f, ...)
 13. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 14. │     ├─purrr:::with_indexed_errors(...)
 15. │     │ └─base::withCallingHandlers(...)
 16. │     ├─purrr:::call_with_cleanup(...)
 17. │     └─shinyCohortBuilder (local) .f(.x[[i]], ...)
 18. │       ├─filter$gui
 19. │       └─S7:::`$.S7_object`(filter, "gui")
 20. │         └─base::stop(msg, call. = FALSE)
 21. └─base::.handleSimpleError(...)
 22.   └─purrr (local) h(simpleError(msg, call))
 23.     └─cli::cli_abort(...)
 24.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [2s] OK
  Running 'testthat.R' [2s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s] ERROR
Error(s) in re-building vignettes:
--- re-building 'custom-gui-layer.Rmd' using rmarkdown
--- finished re-building 'custom-gui-layer.Rmd'

--- re-building 'gui-filter-layer.Rmd' using rmarkdown

Quitting from gui-filter-layer.Rmd:38-41 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `species_filter()`:
! could not find function "species_filter"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gui-filter-layer.Rmd' failed with diagnostics:
could not find function "species_filter"
--- failed re-building 'gui-filter-layer.Rmd'

--- re-building 'package-options.Rmd' using rmarkdown
--- finished re-building 'package-options.Rmd'

--- re-building 'shinyCohortBuilder.Rmd' using rmarkdown

Quitting from shinyCohortBuilder.Rmd:199-205 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map()`:
ℹ In index: 1.
ℹ With name: iris-SepalLength.
Caused by error:
! Can't get S7 properties with `$`. Did you mean `filter@gui`?
---
Backtrace:
     ▆
  1. ├─cohortBuilder::cohort(iris_source)
  2. │ └─Cohort$new(...) at cohortBuilder/R/cohort_methods.R:1297:3
  3. │   └─cohortBuilder (local) initialize(...)
  4. │     └─private$init_source(source, ...) at cohortBuilder/R/cohort_methods.R:47:9
  5. │       └─cohortBuilder:::run_hooks(hook$post, self, private, ...) at cohortBuilder/R/cohort_methods.R:1266:7
  6. │         └─shinyCohortBuilder (local) hook(...) at cohortBuilder/R/hooks.R:116:7
  7. │           └─public$modify(...)
  8. │             └─shinyCohortBuilder (local) modifier(self, private) at cohortBuilder/R/cohort_methods.R:1212:7
  9. │               └─shinyCohortBuilder:::attach_filters_gui(private$steps[[step_id]])
 10. │                 └─step$filters %>% purrr::modify(attach_filter_gui)
 11. └─purrr::modify(., attach_filter_gui)
 12.   └─purrr::map(vec_proxy(.x), .f, ...)
 13.     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 14.       ├─purrr:::with_indexed_errors(...)
 15.       │ └─base::withCallingHandlers(...)
 16.       ├─purrr:::call_with_cleanup(...)
 17.       └─shinyCohortBuilder (local) .f(.x[[i]], ...)
 18.         ├─filter$gui
 19.         └─S7:::`$.S7_object`(filter, "gui")
 20.           └─base::stop(msg, call. = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'shinyCohortBuilder.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: iris-SepalLength.
Caused by error:
! Can't get S7 properties with `$`. Did you mean `filter@gui`?
--- failed re-building 'shinyCohortBuilder.Rmd'

--- re-building 'updating-source.Rmd' using rmarkdown
--- finished re-building 'updating-source.Rmd'

SUMMARY: processing the following files failed:
  'gui-filter-layer.Rmd' 'shinyCohortBuilder.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 2 ERRORs, 1 NOTE