##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cytoviewer.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cytoviewer_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cytoviewer.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cytoviewer/DESCRIPTION’ ... OK
* this is package ‘cytoviewer’ version ‘1.9.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cytoviewer’ 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 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 ... OK
* checking Rd files ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   42. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   43. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   44. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   45. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   46. ├─methods:::.extendsForS3(`<chr>`)
   47. │ └─methods::extends(Class, maybe = FALSE)
   48. │   └─methods::getClassDef(class1)
   49. │     └─methods:::.requirePackage(package)
   50. │       └─base::stop(...)
   51. └─base::.handleSimpleError(...)
   52.   └─shiny (local) h(simpleError(msg, call))
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 91 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘cytoviewer.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from cytoviewer.Rmd:306-316 [dataset]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(...)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   ├─knitr:::in_input_dir(...)
 18. │                   │ └─knitr:::in_dir(input_dir(), expr)
 19. │                   └─knitr (local) evaluate(...)
 20. │                     └─evaluate::evaluate(...)
 21. │                       ├─base::withRestarts(...)
 22. │                       │ └─base (local) withRestartList(expr, restarts)
 23. │                       │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24. │                       │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25. │                       │   └─base (local) withRestartList(expr, restarts[-nr])
 26. │                       │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27. │                       │       └─base (local) doWithOneRestart(return(expr), restart)
 28. │                       ├─evaluate:::with_handlers(...)
 29. │                       │ ├─base::eval(call)
 30. │                       │ │ └─base::eval(call)
 31. │                       │ └─base::withCallingHandlers(...)
 32. │                       └─watcher$print_value(ev$value, ev$visible, envir)
 33. │                         ├─base::withVisible(handle_value(handler, value, visible, envir))
 34. │                         └─evaluate:::handle_value(handler, value, visible, envir)
 35. │                           └─handler$value(value, visible)
 36. │                             └─knitr (local) fun(x, options = options)
 37. │                               ├─base::withVisible(knit_print(x, ...))
 38. │                               ├─knitr::knit_print(x, ...)
 39. │                               └─knitr:::knit_print.default(x, ...)
 40. │                                 └─knitr::normal_print(x)
 41. │                                   ├─methods::show(x)
 42. │                                   └─methods::show(x)
 43. │                                     ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object))
 44. │                                     │ └─base::ifelse(nzchar(vals), vals, "''")
 45. │                                     ├─SingleCellExperiment::reducedDimNames(object)
 46. │                                     └─SingleCellExperiment::reducedDimNames(object)
 47. │                                       └─SingleCellExperiment:::.get_internal_names(...)
 48. │                                         ├─BiocGenerics::updateObject(x)
 49. │                                         └─SingleCellExperiment::updateObject(x)
 50. │                                           ├─methods::callNextMethod()
 51. │                                           └─SummarizedExperiment (local) .nextMethod(object = object)
 52. │                                             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 53. │                                             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 54. │                                               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 55. │                                               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 56. │                                                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 57. └─methods:::.extendsForS3(`<chr>`)
 58.   └─methods::extends(Class, maybe = FALSE)
 59.     └─methods::getClassDef(class1)
 60.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cytoviewer.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘cytoviewer.Rmd’

SUMMARY: processing the following file failed:
  ‘cytoviewer.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/cytoviewer.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL cytoviewer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘cytoviewer’ ...
** this is package ‘cytoviewer’ version ‘1.9.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cytoviewer)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cytoviewer)
> 
> test_check("cytoviewer")
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 91 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_cytoviewer_reactive.R:198:5'): cytoviewer: plot input 3 testing works ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test_cytoviewer_reactive.R:170:3
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   ├─shiny::captureStackTraces(...)
 13. │ │ │   │ └─promises::with_promise_domain(...)
 14. │ │ │   │   └─domain$wrapSync(expr)
 15. │ │ │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
 16. │ │ │   └─env$runWith(self, func)
 17. │ │ │     └─shiny (local) contextFunc()
 18. │ │ │       └─shiny::..stacktraceon..(expr)
 19. │ │ ├─shiny::withReactiveDomain(...)
 20. │ │ │ └─promises::with_promise_domain(...)
 21. │ │ │   └─domain$wrapSync(expr)
 22. │ │ │     └─base::force(expr)
 23. │ │ └─withr::with_options(...)
 24. │ │   └─base::force(code)
 25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 26. ├─testthat::expect_silent(...) at test_cytoviewer_reactive.R:198:5
 27. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
 28. │   ├─testthat (local) .capture(...)
 29. │   │ ├─withr::with_output_sink(...)
 30. │   │ │ └─base::force(code)
 31. │   │ ├─base::withCallingHandlers(...)
 32. │   │ └─base::withVisible(code)
 33. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 34. ├─cytoviewer:::.create_image(...)
 35. │ ├─object[, colData(object)[[input$outline_by]] %in% input$select_outline]
 36. │ └─object[, colData(object)[[input$outline_by]] %in% input$select_outline]
 37. │   ├─BiocGenerics::updateObject(x)
 38. │   └─SingleCellExperiment::updateObject(x)
 39. │     ├─methods::callNextMethod()
 40. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 41. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 42. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 43. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 44. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 45. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 46. ├─methods:::.extendsForS3(`<chr>`)
 47. │ └─methods::extends(Class, maybe = FALSE)
 48. │   └─methods::getClassDef(class1)
 49. │     └─methods:::.requirePackage(package)
 50. │       └─base::stop(...)
 51. └─base::.handleSimpleError(...)
 52.   └─shiny (local) h(simpleError(msg, call))
── Error ('test_cytoviewer_reactive.R:241:5'): cytoviewer: plot input 4 testing works ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test_cytoviewer_reactive.R:212:3
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   ├─shiny::captureStackTraces(...)
 13. │ │ │   │ └─promises::with_promise_domain(...)
 14. │ │ │   │   └─domain$wrapSync(expr)
 15. │ │ │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
 16. │ │ │   └─env$runWith(self, func)
 17. │ │ │     └─shiny (local) contextFunc()
 18. │ │ │       └─shiny::..stacktraceon..(expr)
 19. │ │ ├─shiny::withReactiveDomain(...)
 20. │ │ │ └─promises::with_promise_domain(...)
 21. │ │ │   └─domain$wrapSync(expr)
 22. │ │ │     └─base::force(expr)
 23. │ │ └─withr::with_options(...)
 24. │ │   └─base::force(code)
 25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 26. ├─testthat::expect_silent(...) at test_cytoviewer_reactive.R:241:5
 27. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
 28. │   ├─testthat (local) .capture(...)
 29. │   │ ├─withr::with_output_sink(...)
 30. │   │ │ └─base::force(code)
 31. │   │ ├─base::withCallingHandlers(...)
 32. │   │ └─base::withVisible(code)
 33. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 34. ├─cytoviewer:::.create_image(...)
 35. │ └─cytomapper::plotPixels(...)
 36. │   └─cytomapper:::.outlineImageByMeta(...)
 37. │     ├─object[, colData(object)[, img_id] == mcols(mask)[i, img_id]]
 38. │     └─object[, colData(object)[, img_id] == mcols(mask)[i, img_id]]
 39. │       ├─BiocGenerics::updateObject(x)
 40. │       └─SingleCellExperiment::updateObject(x)
 41. │         ├─methods::callNextMethod()
 42. │         └─SummarizedExperiment (local) .nextMethod(object = object)
 43. │           ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 44. │           └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 45. │             ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 46. │             └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 47. │               └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 48. ├─methods:::.extendsForS3(`<chr>`)
 49. │ └─methods::extends(Class, maybe = FALSE)
 50. │   └─methods::getClassDef(class1)
 51. │     └─methods:::.requirePackage(package)
 52. │       └─base::stop(...)
 53. └─base::.handleSimpleError(...)
 54.   └─shiny (local) h(simpleError(msg, call))
── Error ('test_cytoviewer_reactive.R:319:5'): cytoviewer: plot input 6 testing works ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test_cytoviewer_reactive.R:296:3
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   ├─shiny::captureStackTraces(...)
 13. │ │ │   │ └─promises::with_promise_domain(...)
 14. │ │ │   │   └─domain$wrapSync(expr)
 15. │ │ │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
 16. │ │ │   └─env$runWith(self, func)
 17. │ │ │     └─shiny (local) contextFunc()
 18. │ │ │       └─shiny::..stacktraceon..(expr)
 19. │ │ ├─shiny::withReactiveDomain(...)
 20. │ │ │ └─promises::with_promise_domain(...)
 21. │ │ │   └─domain$wrapSync(expr)
 22. │ │ │     └─base::force(expr)
 23. │ │ └─withr::with_options(...)
 24. │ │   └─base::force(code)
 25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 26. ├─testthat::expect_silent(...) at test_cytoviewer_reactive.R:319:5
 27. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
 28. │   ├─testthat (local) .capture(...)
 29. │   │ ├─withr::with_output_sink(...)
 30. │   │ │ └─base::force(code)
 31. │   │ ├─base::withCallingHandlers(...)
 32. │   │ └─base::withVisible(code)
 33. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 34. ├─cytoviewer:::.create_cells(...)
 35. │ └─cytoviewer:::.subset_object(input, object)
 36. │   ├─object[, colData(object)[[input$color_by]] %in% input$color_by_selection]
 37. │   └─object[, colData(object)[[input$color_by]] %in% input$color_by_selection]
 38. │     ├─BiocGenerics::updateObject(x)
 39. │     └─SingleCellExperiment::updateObject(x)
 40. │       ├─methods::callNextMethod()
 41. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 42. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 43. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 44. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 45. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 46. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 47. ├─methods:::.extendsForS3(`<chr>`)
 48. │ └─methods::extends(Class, maybe = FALSE)
 49. │   └─methods::getClassDef(class1)
 50. │     └─methods:::.requirePackage(package)
 51. │       └─base::stop(...)
 52. └─base::.handleSimpleError(...)
 53.   └─shiny (local) h(simpleError(msg, call))
── Error ('test_cytoviewer_reactive.R:356:5'): cytoviewer: plot input 7 testing works ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test_cytoviewer_reactive.R:333:3
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   ├─shiny::captureStackTraces(...)
 13. │ │ │   │ └─promises::with_promise_domain(...)
 14. │ │ │   │   └─domain$wrapSync(expr)
 15. │ │ │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
 16. │ │ │   └─env$runWith(self, func)
 17. │ │ │     └─shiny (local) contextFunc()
 18. │ │ │       └─shiny::..stacktraceon..(expr)
 19. │ │ ├─shiny::withReactiveDomain(...)
 20. │ │ │ └─promises::with_promise_domain(...)
 21. │ │ │   └─domain$wrapSync(expr)
 22. │ │ │     └─base::force(expr)
 23. │ │ └─withr::with_options(...)
 24. │ │   └─base::force(code)
 25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 26. ├─testthat::expect_silent(...) at test_cytoviewer_reactive.R:356:5
 27. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
 28. │   ├─testthat (local) .capture(...)
 29. │   │ ├─withr::with_output_sink(...)
 30. │   │ │ └─base::force(code)
 31. │   │ ├─base::withCallingHandlers(...)
 32. │   │ └─base::withVisible(code)
 33. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 34. ├─cytoviewer:::.create_cells(...)
 35. │ └─cytoviewer:::.subset_object(input, object)
 36. │   ├─object[, colData(object)[[input$color_by]] %in% input$color_by_selection]
 37. │   └─object[, colData(object)[[input$color_by]] %in% input$color_by_selection]
 38. │     ├─BiocGenerics::updateObject(x)
 39. │     └─SingleCellExperiment::updateObject(x)
 40. │       ├─methods::callNextMethod()
 41. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 42. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 43. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 44. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 45. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 46. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 47. ├─methods:::.extendsForS3(`<chr>`)
 48. │ └─methods::extends(Class, maybe = FALSE)
 49. │   └─methods::getClassDef(class1)
 50. │     └─methods:::.requirePackage(package)
 51. │       └─base::stop(...)
 52. └─base::.handleSimpleError(...)
 53.   └─shiny (local) h(simpleError(msg, call))
── Error ('test_cytoviewer_reactive.R:391:5'): cytoviewer: plot input 8 testing works ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test_cytoviewer_reactive.R:370:3
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   ├─shiny::captureStackTraces(...)
 13. │ │ │   │ └─promises::with_promise_domain(...)
 14. │ │ │   │   └─domain$wrapSync(expr)
 15. │ │ │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
 16. │ │ │   └─env$runWith(self, func)
 17. │ │ │     └─shiny (local) contextFunc()
 18. │ │ │       └─shiny::..stacktraceon..(expr)
 19. │ │ ├─shiny::withReactiveDomain(...)
 20. │ │ │ └─promises::with_promise_domain(...)
 21. │ │ │   └─domain$wrapSync(expr)
 22. │ │ │     └─base::force(expr)
 23. │ │ └─withr::with_options(...)
 24. │ │   └─base::force(code)
 25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 26. ├─testthat::expect_silent(...) at test_cytoviewer_reactive.R:391:5
 27. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
 28. │   ├─testthat (local) .capture(...)
 29. │   │ ├─withr::with_output_sink(...)
 30. │   │ │ └─base::force(code)
 31. │   │ ├─base::withCallingHandlers(...)
 32. │   │ └─base::withVisible(code)
 33. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 34. ├─cytoviewer:::.create_cells(...)
 35. │ ├─...[]
 36. │ └─...[]
 37. │   ├─BiocGenerics::updateObject(x)
 38. │   └─SingleCellExperiment::updateObject(x)
 39. │     ├─methods::callNextMethod()
 40. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 41. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 42. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 43. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 44. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 45. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 46. ├─methods:::.extendsForS3(`<chr>`)
 47. │ └─methods::extends(Class, maybe = FALSE)
 48. │   └─methods::getClassDef(class1)
 49. │     └─methods:::.requirePackage(package)
 50. │       └─base::stop(...)
 51. └─base::.handleSimpleError(...)
 52.   └─shiny (local) h(simpleError(msg, call))

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 91 ]
Error: Test failures
Execution halted