* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MaGPlot.Rcheck’ * using R Under development (unstable) (2024-10-04 r87208) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘MaGPlot/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MaGPlot’ version ‘0.1.0’ * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘CHOUKRI ’ New submission No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "CHOUKRI", family = "Ahmed", role = "aut"), person(family = "CHOUKRI", role = "cre", email = "choukriahmed.uca@yahoo.com")) as necessary. The Description field should not start with the package name, 'This package' or similar. * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... WARNING Found the following files with non-portable file names: Output/Dose_Responses_Plot_Pram121_(±)-GR24.png Output/Dose_Responses_Plot_Pram121_(±)-cannalactone.png Output/Dose_Responses_Plot_Pram121_(±)-epi-cannalactone.png Output/Dose_Responses_Plot_Pram123_(±)-GR24.png Output/Dose_Responses_Plot_Pram123_(±)-cannalactone.png Output/Dose_Responses_Plot_Pram123_(±)-epi-cannalactone.png Output/Dose_Responses_Plot_Pram127_(±)-GR24.png Output/Dose_Responses_Plot_Pram127_(±)-cannalactone.png Output/Dose_Responses_Plot_Pram127_(±)-epi-cannalactone.png Output/Dose_Responses_Plot_jpm_(±)-GR24.png Output/Dose_Responses_Plot_jpm_(±)-cannalactone.png Output/Dose_Responses_Plot_jpm_(±)-epi-cannalactone.png Output/Dose_Responses_Plot_koiz_(±)-GR24.png Output/Dose_Responses_Plot_koiz_(±)-cannalactone.png Output/Dose_Responses_Plot_koiz_(±)-epi-cannalactone.png Output/Dose_Responses_Plot_zae_(±)-GR24.png Output/Dose_Responses_Plot_zae_(±)-cannalactone.png Output/Dose_Responses_Plot_zae_(±)-epi-cannalactone.png Example dataset These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘MaGPlot’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘Example dataset’ ‘Output’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘RColorBrewer’ ‘cowplot’ ‘dplyr’ ‘ggplot2’ ‘ggplotify’ ‘pheatmap’ ‘tidyr’ 'library' or 'require' calls in package code: ‘RColorBrewer’ ‘cowplot’ ‘dplyr’ ‘ggplot2’ ‘ggplotify’ ‘pheatmap’ ‘tidyr’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] NOTE PCA: no visible global function definition for ‘read_excel’ PCA: no visible global function definition for ‘%>%’ PCA: no visible global function definition for ‘mutate’ PCA: no visible binding for global variable ‘MaxResponse’ PCA: no visible binding for global variable ‘EC50’ PCA: no visible binding for global variable ‘Molecule’ PCA: no visible binding for global variable ‘Genotype’ PCA: no visible global function definition for ‘group_by’ PCA: no visible global function definition for ‘summarise’ PCA: no visible global function definition for ‘left_join’ PCA: no visible global function definition for ‘prcomp’ PCA: no visible binding for '<<-' assignment to ‘pca_plot’ PCA: no visible global function definition for ‘ggplot’ PCA: no visible global function definition for ‘aes’ PCA: no visible binding for global variable ‘PC1’ PCA: no visible binding for global variable ‘PC2’ PCA: no visible global function definition for ‘geom_point’ PCA: no visible global function definition for ‘geom_text_repel’ PCA: no visible global function definition for ‘labs’ PCA: no visible global function definition for ‘theme_minimal’ PCA: no visible global function definition for ‘theme’ PCA: no visible global function definition for ‘element_text’ PCA: no visible global function definition for ‘guides’ PCA: no visible global function definition for ‘guide_legend’ PCA: no visible global function definition for ‘dev.new’ PCA: no visible binding for global variable ‘pca_plot’ adjust_data: no visible global function definition for ‘%>%’ adjust_data: no visible global function definition for ‘group_by’ adjust_data: no visible binding for global variable ‘Genotype’ adjust_data: no visible global function definition for ‘summarise’ adjust_data: no visible binding for global variable ‘Response’ adjust_data: no visible binding for global variable ‘Molecule’ adjust_data: no visible global function definition for ‘left_join’ adjust_data: no visible global function definition for ‘mutate’ adjust_data: no visible binding for global variable ‘mean_negative_control’ adjust_data: no visible binding for global variable ‘mean_positive_control’ adjust_data: no visible global function definition for ‘select’ check_and_install_packages: no visible global function definition for ‘installed.packages’ check_and_install_packages: no visible global function definition for ‘install.packages’ comp: no visible global function definition for ‘filter’ comp: no visible binding for global variable ‘Response’ comp: no visible binding for global variable ‘Molecule’ comp: no visible binding for global variable ‘Genotype’ comp: no visible global function definition for ‘%>%’ comp: no visible binding for global variable ‘Concentration’ comp: no visible global function definition for ‘drda’ comp: no visible global function definition for ‘anova’ comp: no visible global function definition for ‘coef’ comp: no visible global function definition for ‘vcov’ comp: no visible global function definition for ‘png’ comp: no visible global function definition for ‘grid’ comp: no visible global function definition for ‘dev.off’ comp: no visible global function definition for ‘createWorkbook’ comp: no visible global function definition for ‘addWorksheet’ comp: no visible global function definition for ‘writeData’ comp: no visible global function definition for ‘capture.output’ generate_plots: no visible global function definition for ‘png’ generate_plots: no visible global function definition for ‘qqnorm’ generate_plots: no visible global function definition for ‘qqline’ generate_plots: no visible global function definition for ‘dev.off’ generate_plots: no visible global function definition for ‘density’ perform_clustering: no visible global function definition for ‘read_excel’ perform_clustering: no visible global function definition for ‘%>%’ perform_clustering: no visible global function definition for ‘mutate’ perform_clustering: no visible binding for global variable ‘MaxResponse’ perform_clustering: no visible binding for global variable ‘EC50’ perform_clustering: no visible binding for global variable ‘Molecule’ perform_clustering: no visible binding for global variable ‘Genotype’ perform_clustering: no visible global function definition for ‘distinct’ perform_clustering: no visible global function definition for ‘filter_all’ perform_clustering: no visible global function definition for ‘all_vars’ perform_clustering: no visible binding for global variable ‘.’ perform_clustering: no visible global function definition for ‘sd’ perform_clustering: no visible global function definition for ‘daisy’ perform_clustering: no visible global function definition for ‘hclust’ perform_clustering: no visible global function definition for ‘as.dendrogram’ perform_clustering: no visible global function definition for ‘color_branches’ perform_clustering: no visible global function definition for ‘color_labels’ perform_clustering: no visible global function definition for ‘labels<-’ pltt: no visible global function definition for ‘ggplot’ pltt: no visible global function definition for ‘aes’ pltt: no visible binding for global variable ‘EC50’ pltt: no visible binding for global variable ‘Molecule’ pltt: no visible binding for global variable ‘Genotype’ pltt: no visible global function definition for ‘geom_bar’ pltt: no visible global function definition for ‘position_dodge’ pltt: no visible global function definition for ‘geom_errorbar’ pltt: no visible binding for global variable ‘SE_EC50’ pltt: no visible global function definition for ‘geom_text’ pltt: no visible binding for global variable ‘EC50_Letters’ pltt: no visible global function definition for ‘scale_x_continuous’ pltt: no visible global function definition for ‘coord_cartesian’ pltt: no visible global function definition for ‘labs’ pltt: no visible global function definition for ‘theme_minimal’ pltt: no visible global function definition for ‘theme’ pltt: no visible global function definition for ‘element_blank’ pltt: no visible global function definition for ‘element_text’ pltt: no visible global function definition for ‘element_line’ pltt: no visible global function definition for ‘element_rect’ pltt: no visible global function definition for ‘scale_y_discrete’ pltt: no visible global function definition for ‘scale_fill_brewer’ pltt: no visible binding for global variable ‘MaxResponse’ pltt: no visible binding for global variable ‘SE_MaxResponse’ pltt: no visible binding for global variable ‘MaxResponse_Letters’ pltt: no visible global function definition for ‘dcast’ pltt: no visible global function definition for ‘pheatmap’ pltt: no visible global function definition for ‘colorRampPalette’ pltt: no visible global function definition for ‘brewer.pal’ pltt: no visible global function definition for ‘ggsave’ pltt: no visible global function definition for ‘save_plot’ pltt: no visible global function definition for ‘plot_grid’ pltt: no visible global function definition for ‘dev.new’ pltt_with_nc: no visible global function definition for ‘%>%’ pltt_with_nc: no visible global function definition for ‘mutate’ pltt_with_nc: no visible binding for global variable ‘SE_EC50’ pltt_with_nc: no visible binding for global variable ‘SE_EC50_Filtered’ pltt_with_nc: no visible binding for global variable ‘EC50_Letters’ pltt_with_nc: no visible global function definition for ‘ggplot’ pltt_with_nc: no visible global function definition for ‘aes’ pltt_with_nc: no visible binding for global variable ‘EC50’ pltt_with_nc: no visible binding for global variable ‘Molecule’ pltt_with_nc: no visible binding for global variable ‘Genotype’ pltt_with_nc: no visible global function definition for ‘geom_bar’ pltt_with_nc: no visible global function definition for ‘position_dodge’ pltt_with_nc: no visible global function definition for ‘geom_errorbar’ pltt_with_nc: no visible global function definition for ‘geom_text’ pltt_with_nc: no visible global function definition for ‘scale_x_continuous’ pltt_with_nc: no visible global function definition for ‘coord_cartesian’ pltt_with_nc: no visible global function definition for ‘labs’ pltt_with_nc: no visible global function definition for ‘theme_minimal’ pltt_with_nc: no visible global function definition for ‘theme’ pltt_with_nc: no visible global function definition for ‘element_blank’ pltt_with_nc: no visible global function definition for ‘element_text’ pltt_with_nc: no visible global function definition for ‘element_line’ pltt_with_nc: no visible global function definition for ‘element_rect’ pltt_with_nc: no visible global function definition for ‘scale_y_discrete’ pltt_with_nc: no visible global function definition for ‘scale_fill_brewer’ pltt_with_nc: no visible binding for global variable ‘MaxResponse’ pltt_with_nc: no visible binding for global variable ‘SE_MaxResponse’ pltt_with_nc: no visible binding for global variable ‘MaxResponse_Letters’ pltt_with_nc: no visible global function definition for ‘dcast’ pltt_with_nc: no visible global function definition for ‘pheatmap’ pltt_with_nc: no visible global function definition for ‘colorRampPalette’ pltt_with_nc: no visible global function definition for ‘brewer.pal’ pltt_with_nc: no visible global function definition for ‘ggsave’ pltt_with_nc: no visible global function definition for ‘save_plot’ pltt_with_nc: no visible global function definition for ‘plot_grid’ pltt_with_nc: no visible global function definition for ‘dev.new’ run_statistical_tests: no visible global function definition for ‘shapiro.test’ run_statistical_tests: no visible global function definition for ‘dip.test’ st : calculate_t_test: no visible global function definition for ‘pt’ st: no visible binding for '<<-' assignment to ‘comparisons_ec50’ st: no visible binding for '<<-' assignment to ‘comparisons_maxresponse’ st: no visible global function definition for ‘%>%’ st: no visible binding for global variable ‘comparisons_ec50’ st: no visible global function definition for ‘add_row’ st: no visible binding for global variable ‘comparisons_maxresponse’ st: no visible global function definition for ‘createWorkbook’ st: no visible global function definition for ‘addWorksheet’ st: no visible global function definition for ‘writeData’ st: no visible global function definition for ‘saveWorkbook’ Undefined global functions or variables: %>% . Concentration EC50 EC50_Letters Genotype MaxResponse MaxResponse_Letters Molecule PC1 PC2 Response SE_EC50 SE_EC50_Filtered SE_MaxResponse addWorksheet add_row aes all_vars anova as.dendrogram brewer.pal capture.output coef colorRampPalette color_branches color_labels comparisons_ec50 comparisons_maxresponse coord_cartesian createWorkbook daisy dcast density dev.new dev.off dip.test distinct drda element_blank element_line element_rect element_text filter filter_all geom_bar geom_errorbar geom_point geom_text geom_text_repel ggplot ggsave grid group_by guide_legend guides hclust install.packages installed.packages labels<- labs left_join mean_negative_control mean_positive_control mutate pca_plot pheatmap plot_grid png position_dodge prcomp pt qqline qqnorm read_excel saveWorkbook save_plot scale_fill_brewer scale_x_continuous scale_y_discrete sd select shapiro.test summarise theme theme_minimal vcov writeData Consider adding importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off", "png") importFrom("graphics", "grid") importFrom("stats", "anova", "as.dendrogram", "coef", "density", "filter", "hclust", "prcomp", "pt", "qqline", "qqnorm", "sd", "shapiro.test", "vcov") importFrom("utils", "capture.output", "install.packages", "installed.packages") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘PCA’ ‘check_and_install_packages’ ‘comp’ ‘perform_clustering’ ‘pltt’ ‘pltt_with_nc’ ‘st’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Functions or methods with usage in Rd file 'analyze_dose_response.Rd' but not in code: ‘analyze_dose_response’ Functions or methods with usage in Rd file 'calculate_t_test.Rd' but not in code: ‘calculate_t_test’ Functions or methods with usage in Rd file 'combine_save_plots.Rd' but not in code: ‘combine_save_plots’ Functions or methods with usage in Rd file 'export_to_excel.Rd' but not in code: ‘export_to_excel’ Functions or methods with usage in Rd file 'generate_ec50_heatmap.Rd' but not in code: ‘generate_ec50_heatmap’ Functions or methods with usage in Rd file 'generate_max_response_heatmap.Rd' but not in code: ‘generate_max_response_heatmap’ Functions or methods with usage in Rd file 'plot_ec50.Rd' but not in code: ‘plot_ec50’ Functions or methods with usage in Rd file 'plot_max_response.Rd' but not in code: ‘plot_max_response’ Functions or methods with usage in Rd file 'rank_groups.Rd' but not in code: ‘rank_groups’ Functions or methods with usage in Rd file 'save_plot.Rd' but not in code: ‘save_plot’ * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MaGPlot.Rmd’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... NONE * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 6 WARNINGs, 4 NOTEs