############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/PeacoQC.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PeacoQC/DESCRIPTION’ ... OK * this is package ‘PeacoQC’ version ‘1.6.0’ * 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 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 24.004 0.196 24.245 PeacoQCHeatmap 11.047 0.069 11.138 PeacoQC 10.115 0.245 10.377 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.15-bioc/meat/PeacoQC.Rcheck/00check.log’ for details.