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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crisprShiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crisprShiny_1.7.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/crisprShiny.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprShiny/DESCRIPTION’ ... OK
* this is package ‘crisprShiny’ version ‘1.7.1’
* 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 ‘crisprShiny’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  guideSetExample_basic.Rd: GuideSet-class
  guideSetExample_kras.Rd: GuideSet-class
  guideSetExample_kras_be.Rd: GuideSet-class
  guideSetExample_ntcs.Rd: GuideSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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:
   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_true(length(gs_filtered()) == 0) at test-utils_filters.R:157:9
  
  [ FAIL 3 | WARN 2 | SKIP 10 | PASS 300 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/crisprShiny.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crisprShiny
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘crisprShiny’ ...
** this is package ‘crisprShiny’ version ‘1.7.1’
** using staged installation
** R
** data
** 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 (crisprShiny)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(crisprShiny)
Loading required package: shiny
> 
> test_check("crisprShiny")
Loading required package: crisprBase

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'Biostrings'

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

    strsplit

Saving _problems/test-interface_tooltips-42.R
Saving _problems/test-utils_filters-155.R
Saving _problems/test-utils_filters-157.R
[ FAIL 3 | WARN 2 | SKIP 10 | PASS 300 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• Long render time for browser plot (2): 'test-interface_alignments.R:108:5',
  'test-interface_guideBrowser.R:30:5'
• On CRAN (1): 'test-interface_guideBrowser.R:86:1'
• empty test (7): 'test-crisprServer.R:38:1',
  'test-interface_alignments.R:1:1', 'test-interface_guideBrowser.R:1:1',
  'test-interface_tooltips.R:1:1', 'test-utils_alignments.R:181:1',
  'test-utils_filters.R:184:1', 'test-utils_filters.R:191:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-interface_tooltips.R:41:5'): .dtTooltipText retrieves tooltip text ──
Expected `grepl("azimuth method", .dtTooltipText("score_azimuth"), ignore.case = TRUE)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

── Failure ('test-utils_filters.R:155:9'): .applyGuideSetFilters apply score filters ──
Expected `all(gs_filtered()$score_azimuth >= 0.5)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test-utils_filters.R:152:5
  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_true(all(gs_filtered()$score_azimuth >= 0.5)) at test-utils_filters.R:155:9
── Failure ('test-utils_filters.R:157:9'): .applyGuideSetFilters apply score filters ──
Expected `length(gs_filtered()) == 0` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test-utils_filters.R:152:5
  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_true(length(gs_filtered()) == 0) at test-utils_filters.R:157:9

[ FAIL 3 | WARN 2 | SKIP 10 | PASS 300 ]
Error:
! Test failures.
Execution halted