• 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 See the install log for details.
• 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
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• 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
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• 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