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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PeacoQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PeacoQC_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/PeacoQC.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PeacoQC/DESCRIPTION’ ... OK
* this is package ‘PeacoQC’ version ‘1.21.0’
* 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 ‘PeacoQC’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘flowWorkspace’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BuildBackgroundQCPlot: no visible binding for global variable ‘x_min’
BuildBackgroundQCPlot: no visible binding for global variable ‘x_max’
BuildBackgroundQCPlot: no visible binding for global variable ‘y_min’
BuildBackgroundQCPlot: no visible binding for global variable ‘y_max’
BuildBackgroundQCPlot: no visible binding for global variable
  ‘fill_blocks’
BuildChannelPlots: no visible binding for global variable ‘Cells’
BuildManualPartPlot: no visible binding for global variable ‘minimum’
BuildManualPartPlot: no visible binding for global variable ‘x_min’
BuildManualPartPlot: no visible binding for global variable ‘x_max’
BuildManualPartPlot: no visible binding for global variable ‘y_min’
BuildManualPartPlot: no visible binding for global variable ‘y_max’
BuildPeaksPlot: no visible binding for global variable ‘Bin’
BuildPeaksPlot: no visible binding for global variable ‘Peak’
BuildPeaksPlot: no visible binding for global variable ‘Cluster’
BuildTimePlot: no visible binding for global variable ‘x_min’
BuildTimePlot: no visible binding for global variable ‘x_max’
BuildTimePlot: no visible binding for global variable ‘y_min’
BuildTimePlot: no visible binding for global variable ‘y_max’
BuildTimePlot: no visible binding for global variable ‘fill_blocks’
Undefined global functions or variables:
  Bin Cells Cluster Peak fill_blocks minimum x_max x_min y_max y_min
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'PlotPeacoQC.Rd':
PlotPeacoQC
  Code: function(ff, channels, output_directory = ".", display_cells =
                 2000, manual_cells = NULL, title_FR = NULL,
                 display_peaks = TRUE, prefix = "PeacoQC_", time_unit =
                 GetTimeUnit(ff), time_channel_parameter = "Time", ...)
  Docs: function(ff, channels, output_directory = ".", display_cells =
                 2000, manual_cells = NULL, title_FR = NULL,
                 display_peaks = TRUE, prefix = "PeacoQC_", time_unit =
                 100, time_channel_parameter = "Time", ...)
  Mismatches in argument default values:
    Name: 'time_unit' Code: GetTimeUnit(ff) Docs: 100

Codoc mismatches from Rd file 'RemoveDoublets.Rd':
RemoveDoublets
  Code: function(ff, channel1 = "FSC-A", channel2 = "FSC-H", nmad = 4,
                 verbose = FALSE, output = "frame", b = 0)
  Docs: function(ff, channel1 = "FSC-A", channel2 = "FSC-H", nmad = 4,
                 verbose = FALSE, output = "frame")
  Argument names in code not in docs:
    b

Codoc mismatches from Rd file 'RemoveMargins.Rd':
RemoveMargins
  Code: function(ff, channels, channel_specifications = NULL, output =
                 "frame", remove_min = channels, remove_max = channels)
  Docs: function(ff, channels, channel_specifications = NULL, output =
                 "frame")
  Argument names in code not in docs:
    remove_min remove_max

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'RemoveDoublets.Rd':
  ‘b’

Documented arguments not in \usage in Rd file 'RemoveMargins.Rd':
  ‘remove_min’ ‘remove_max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
PlotPeacoQC 7.707  0.068   7.943
* 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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/PeacoQC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PeacoQC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘PeacoQC’ ...
** this is package ‘PeacoQC’ version ‘1.21.0’
** 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 (PeacoQC)