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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:PeacoQC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings PeacoQC_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/PeacoQC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘PeacoQC/DESCRIPTION’ ... OK
* this is package ‘PeacoQC’ version ‘1.8.0’
* 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 R 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 ... 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 documentation object 'PeacoQC':
PeacoQC
  Code: function(ff, channels, determine_good_cells = "all", plot = 20,
                 save_fcs = TRUE, output_directory = ".",
                 name_directory = "PeacoQC_results", report = TRUE,
                 events_per_bin = FindEventsPerBin(remove_zeros, ff,
                 channels, min_cells, max_bins, step), min_cells = 150,
                 max_bins = 500, step = 500, MAD = 6, IT_limit = 0.6,
                 consecutive_bins = 5, remove_zeros = FALSE, suffix_fcs
                 = "_QC", force_IT = 150, peak_removal = (1/3),
                 min_nr_bins_peakdetection = 10, time_channel_parameter
                 = "Time", ...)
  Docs: function(ff, channels, determine_good_cells = "all", plot = 20,
                 save_fcs = TRUE, output_directory = ".",
                 name_directory = "PeacoQC_results", report = TRUE,
                 events_per_bin = FindEventsPerBin(remove_zeros, ff,
                 channels, min_cells, max_bins, step), min_cells = 150,
                 max_bins = 500, step = 500, MAD = 6, IT_limit = 0.6,
                 consecutive_bins = 5, remove_zeros = FALSE, suffix_fcs
                 = "_QC", force_IT = 150, peak_removal = (1/3),
                 min_nr_bins_peakdetection = 10, ...)
  Argument names in code not in docs:
    time_channel_parameter
  Mismatches in argument names:
    Position: 21 Code: time_channel_parameter Docs: ...

Codoc mismatches from documentation object 'PlotPeacoQC':
PlotPeacoQC
  Code: 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", ...)
  Docs: function(ff, channels, output_directory = ".", display_cells =
                 2000, manual_cells = NULL, title_FR = NULL,
                 display_peaks = TRUE, prefix = "PeacoQC_", time_unit =
                 100, ...)
  Argument names in code not in docs:
    time_channel_parameter
  Mismatches in argument names:
    Position: 10 Code: time_channel_parameter Docs: ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
PlotPeacoQC    12.608  0.180  12.790
PeacoQC         5.943  0.287   6.233
PeacoQCHeatmap  5.218  0.143   5.362
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘PeacoQC_Vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/PeacoQC.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL PeacoQC
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘PeacoQC’ ...
** 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)