############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings synergyfinder_3.2.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/synergyfinder.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘synergyfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘synergyfinder’ version ‘3.2.10’ * 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 ‘synergyfinder’ 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 ... WARNING '::' or ':::' import not declared from: ‘scales’ Namespaces in Imports field not imported from: ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’ 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 .Extract2DrugPlotData: no visible binding for global variable ‘input_type’ .Extract2DrugPlotData: no visible binding for global variable ‘block_id’ .Extract2DrugPlotData: no visible binding for global variable ‘value’ .Extract2DrugPlotData: no visible binding for global variable ‘left’ .Extract2DrugPlotData: no visible binding for global variable ‘right’ .Extract2DrugPlotData: no visible binding for global variable ‘conc1’ .Extract2DrugPlotData: no visible binding for global variable ‘conc2’ .Extract2DrugPlotData: no visible binding for global variable ‘text’ .ExtractMultiDrugPlotData: no visible binding for global variable ‘block_id’ Bliss: no visible binding for global variable ‘Bliss_ref’ CalculateCSS: no visible binding for global variable ‘data’ CalculateSensitivity: no visible binding for global variable ‘response_origin’ CalculateSensitivity: no visible binding for global variable ‘block_id’ CalculateSynergy: no visible binding for global variable ‘response_origin’ CalculateSynergy: no visible binding for global variable ‘block_id’ HSA: no visible binding for global variable ‘HSA_ref’ HighlightBarPlot: no visible binding for global variable ‘id’ HighlightBarPlot: no visible binding for global variable ‘value’ HighlightBarPlot: no visible binding for global variable ‘color’ Plot2DrugHeatmap: no visible binding for global variable ‘text’ PlotBarometer: no visible binding for global variable ‘block_id’ PlotBarometer: no visible binding for global variable ‘response_mean’ PlotBarometer: no visible binding for global variable ‘response’ PlotBarometer: no visible binding for global variable ‘r’ PlotBarometer: no visible binding for global variable ‘theta’ PlotBarometer: no visible binding for global variable ‘value’ PlotBarometer: no visible binding for global variable ‘start’ PlotBarometer: no visible binding for global variable ‘end’ PlotBarometer: no visible binding for global variable ‘label’ PlotBarometer: no visible binding for global variable ‘x’ PlotBarometer: no visible binding for global variable ‘y’ PlotBarometer: no visible binding for global variable ‘adjust’ PlotBarometer: no visible binding for global variable ‘angle’ PlotDoseResponseCurve: no visible binding for global variable ‘response_origin’ PlotDoseResponseCurve: no visible binding for global variable ‘block_id’ PlotMultiDrugBar: no visible binding for global variable ‘id’ PlotMultiDrugBar: no visible binding for global variable ‘value’ PlotMultiDrugBar: no visible binding for global variable ‘color’ PlotMultiDrugBar: no visible binding for global variable ‘metric’ PlotSensitivitySynergy: no visible binding for global variable ‘block_id’ PlotSensitivitySynergy: no visible binding for global variable ‘css’ PlotSensitivitySynergy: no visible binding for global variable ‘label’ PlotSensitivitySynergy: no visible binding for global variable ‘synergy’ ReshapeData: no visible binding for global variable ‘block_id’ ReshapeData: no visible binding for global variable ‘n’ ReshapeData: no visible global function definition for ‘head’ ReshapeData: no visible binding for global variable ‘response_origin’ ReshapeData: no visible binding for global variable ‘nn’ ReshapeData: no visible binding for global variable ‘maxn’ ReshapeData: no visible binding for global variable ‘response_sd’ ReshapeData: no visible binding for global variable ‘response_sem’ ReshapeData: no visible binding for global variable ‘response_mean’ ReshapeData: no visible binding for global variable ‘response_CI95’ ReshapeData: no visible binding for global variable ‘response_origin_sd’ ReshapeData: no visible binding for global variable ‘response_origin_sem’ ReshapeData: no visible binding for global variable ‘response_origin_mean’ ReshapeData: no visible binding for global variable ‘response_origin_CI95’ ZIP : : no visible binding for global variable ‘data’ ZIP : : no visible binding for global variable ‘pred’ ZIP : : no visible global function definition for ‘:=’ ZIP: no visible binding for global variable ‘.’ ZIP: no visible binding for global variable ‘ZIP_fit’ ZIP: no visible binding for global variable ‘ZIP_ref’ ZIP: no visible binding for global variable ‘ZIP_synergy’ Undefined global functions or variables: . := Bliss_ref HSA_ref ZIP_fit ZIP_ref ZIP_synergy adjust angle block_id color conc1 conc2 css data end head id input_type label left maxn metric n nn pred r response response_CI95 response_mean response_origin response_origin_CI95 response_origin_mean response_origin_sd response_origin_sem response_sd response_sem right start synergy text theta value x y Consider adding importFrom("graphics", "text") importFrom("stats", "end", "start") importFrom("utils", "data", "head") to your NAMESPACE file. * 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 'PlotDoseResponse': PlotDoseResponse Code: function(data, block_ids = c(1), drugs = c(1, 2), adjusted = TRUE, statistic = NULL, summary_statistic = "mean", high_value_color = "#FF0000", low_value_color = "#00FF00", point_color = "#C24B40", curve_color = "black", curve_ylim = NULL, curve_grid = TRUE, text_size_scale = 1, heatmap_text_label_size_scale = 1, heatmap_text_label_color = "#000000", heatmap_color_range = NULL, curve_plot_title = NULL, heatmap_plot_title = NULL, Emin = NA, Emax = NA, save_file = FALSE, file_type = "pdf", file_name = NULL, width = 12, height = 6) Docs: function(data, block_ids = c(1), drugs = c(1, 2), adjusted = TRUE, statistic = NULL, summary_statistic = "mean", high_value_color = "#A90217", low_value_color = "#2166AC", point_color = "#C24B40", curve_color = "black", curve_ylim = NULL, curve_grid = TRUE, text_size_scale = 1, heatmap_text_label_size_scale = 1, heatmap_text_label_color = "#000000", heatmap_color_range = NULL, curve_plot_title = NULL, heatmap_plot_title = NULL, Emin = NA, Emax = NA, save_file = FALSE, file_type = "pdf", file_name = NULL, width = 12, height = 6) Mismatches in argument default values: Name: 'high_value_color' Code: "#FF0000" Docs: "#A90217" Name: 'low_value_color' Code: "#00FF00" Docs: "#2166AC" Codoc mismatches from documentation object 'PlotSynergy': PlotSynergy Code: function(data, type = "2D", method = "ZIP", block_ids = c(1), drugs = c(1, 2), row_range = NULL, col_range = NULL, color_range = NULL, z_range = NULL, axis_line = FALSE, statistic = NULL, summary_statistic = "mean", plot_title = NULL, interpolate_len = 3, high_value_color = "#FF0000", low_value_color = "#00FF00", text_size_scale = 1, heatmap_text_label_size_scale = 1, heatmap_text_label_color = "#000000", grid = TRUE, dynamic = FALSE, display = TRUE, save_file = FALSE, file_type = "pdf", file_name = NULL, file_path = NULL, height = 6, width = 6, units = "in") Docs: function(data, type = "2D", method = "ZIP", block_ids = c(1), drugs = c(1, 2), row_range = NULL, col_range = NULL, color_range = NULL, z_range = NULL, axis_line = FALSE, statistic = NULL, summary_statistic = "mean", plot_title = NULL, interpolate_len = 3, high_value_color = "#A90217", low_value_color = "#2166AC", text_size_scale = 1, heatmap_text_label_size_scale = 1, heatmap_text_label_color = "#000000", grid = TRUE, dynamic = FALSE, display = TRUE, save_file = FALSE, file_type = "pdf", file_name = NULL, file_path = NULL, height = 6, width = 6, units = "in") Mismatches in argument default values: Name: 'high_value_color' Code: "#FF0000" Docs: "#A90217" Name: 'low_value_color' Code: "#00FF00" Docs: "#2166AC" * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed CalculateSensitivity 43.087 0.342 43.498 PlotMultiDrugSurface 16.260 0.255 16.531 PlotMultiDrugBar 10.135 0.038 10.179 PlotSensitivitySynergy 5.865 0.052 5.925 * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/synergyfinder.Rcheck/00check.log’ for details.