* using log directory ‘/srv/hornik/tmp/CRAN_pretest/diceplot.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 ‘diceplot/DESCRIPTION’ ... OK * this is package ‘diceplot’ version ‘0.0.0.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/2s] NOTE Maintainer: ‘Matthias Flotho ’ New submission Version contains large components (0.0.0.9000) Non-FOSS package license (use_mit_license() license) Possibly misspelled words in DESCRIPTION: continous (10:72) Authors@R field gives persons with deprecated or bad elements: Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. Calls: ... FUN -> with -> with.default -> eval -> eval -> person1 The Title field should be in title case. Current version is: ‘Dice-plot: a package for high dimensional categorical data visualization’ In title case that is: ‘Dice-Plot: a Package for High Dimensional Categorical Data Visualization’ * 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 file with a non-portable file name: R/experiments/test2_almost running.R 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 ‘diceplot’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: use_mit_license() license Standardizable: FALSE Authors@R field gives no person with maintainer role, valid email address and non-empty name. Author field differs from that derived from Authors@R Author: ‘Matthias Flotho’ Authors@R: ‘Matthias matthias.flotho@ccb.uni-saarland.de Flotho [aut, cre] (ORCID: )’ Maintainer field differs from that derived from Authors@R Maintainer: ‘Matthias Flotho ’ Authors@R: ‘’ * 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 ... [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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] NOTE dice_plot: no visible global function definition for ‘theme_minimal’ dice_plot_3: no visible global function definition for ‘theme_minimal’ dice_plot_3: no visible global function definition for ‘%>%’ dice_plot_3: no visible global function definition for ‘group_by’ dice_plot_3: no visible global function definition for ‘sym’ dice_plot_3: no visible global function definition for ‘summarise’ dice_plot_3: no visible global function definition for ‘n_distinct’ dice_plot_3: no visible global function definition for ‘filter’ dice_plot_3: no visible binding for global variable ‘unique_groups’ dice_plot_3: no visible global function definition for ‘ggplot’ dice_plot_3: no visible global function definition for ‘geom_rect’ dice_plot_3: no visible global function definition for ‘aes’ dice_plot_3: no visible binding for global variable ‘x_min’ dice_plot_3: no visible binding for global variable ‘x_max’ dice_plot_3: no visible binding for global variable ‘y_min’ dice_plot_3: no visible binding for global variable ‘y_max’ dice_plot_3: no visible global function definition for ‘geom_point’ dice_plot_3: no visible binding for global variable ‘x_pos’ dice_plot_3: no visible binding for global variable ‘y_pos’ dice_plot_3: no visible global function definition for ‘scale_color_manual’ dice_plot_3: no visible global function definition for ‘scale_fill_manual’ dice_plot_3: no visible global function definition for ‘scale_x_discrete’ dice_plot_3: no visible global function definition for ‘scale_y_discrete’ dice_plot_3: no visible global function definition for ‘theme’ dice_plot_3: no visible global function definition for ‘element_text’ dice_plot_3: no visible global function definition for ‘element_blank’ dice_plot_3: no visible global function definition for ‘unit’ dice_plot_3: no visible global function definition for ‘labs’ dice_plot_3: no visible global function definition for ‘coord_fixed’ dice_plot_3: no visible global function definition for ‘ggtitle’ dice_plot_3: no visible global function definition for ‘guides’ dice_plot_3: no visible global function definition for ‘mutate’ dice_plot_3: no visible binding for global variable ‘x_offset’ dice_plot_3: no visible binding for global variable ‘y_offset’ dice_plot_3: no visible binding for global variable ‘x’ dice_plot_3: no visible binding for global variable ‘y’ dice_plot_3: no visible binding for global variable ‘var’ dice_plot_3: no visible global function definition for ‘theme_void’ dice_plot_3: no visible global function definition for ‘margin’ dice_plot_3: no visible global function definition for ‘coord_cartesian’ dice_plot_3: no visible global function definition for ‘geom_text’ dice_plot_3: no visible global function definition for ‘ggdraw’ dice_plot_3: no visible global function definition for ‘draw_plot’ dice_plot_3: no visible global function definition for ‘ggsave’ dice_plot_4: no visible global function definition for ‘theme_minimal’ dice_plot_4: no visible global function definition for ‘%>%’ dice_plot_4: no visible global function definition for ‘group_by’ dice_plot_4: no visible global function definition for ‘sym’ dice_plot_4: no visible global function definition for ‘summarise’ dice_plot_4: no visible global function definition for ‘n_distinct’ dice_plot_4: no visible global function definition for ‘filter’ dice_plot_4: no visible binding for global variable ‘unique_groups’ dice_plot_4: no visible global function definition for ‘mutate’ dice_plot_4: no visible binding for global variable ‘present’ dice_plot_4: no visible global function definition for ‘unite’ dice_plot_4: no visible global function definition for ‘pivot_wider’ dice_plot_4: no visible binding for global variable ‘combined’ dice_plot_4: no visible binding for global variable ‘value’ dice_plot_4: no visible global function definition for ‘column_to_rownames’ dice_plot_4: no visible global function definition for ‘dist’ dice_plot_4: no visible global function definition for ‘hclust’ dice_plot_4: no visible global function definition for ‘:=’ dice_plot_4: no visible global function definition for ‘n’ dice_plot_4: no visible global function definition for ‘arrange’ dice_plot_4: no visible global function definition for ‘desc’ dice_plot_4: no visible binding for global variable ‘count’ dice_plot_4: no visible global function definition for ‘pull’ dice_plot_4: no visible global function definition for ‘left_join’ dice_plot_4: no visible global function definition for ‘setNames’ dice_plot_4: no visible binding for global variable ‘x_offset’ dice_plot_4: no visible binding for global variable ‘y_offset’ dice_plot_4: no visible global function definition for ‘distinct’ dice_plot_4: no visible global function definition for ‘ggplot’ dice_plot_4: no visible global function definition for ‘geom_rect’ dice_plot_4: no visible global function definition for ‘aes’ dice_plot_4: no visible binding for global variable ‘x_min’ dice_plot_4: no visible binding for global variable ‘x_max’ dice_plot_4: no visible binding for global variable ‘y_min’ dice_plot_4: no visible binding for global variable ‘y_max’ dice_plot_4: no visible global function definition for ‘geom_point’ dice_plot_4: no visible binding for global variable ‘x_pos’ dice_plot_4: no visible binding for global variable ‘y_pos’ dice_plot_4: no visible global function definition for ‘scale_color_manual’ dice_plot_4: no visible global function definition for ‘scale_fill_manual’ dice_plot_4: no visible global function definition for ‘scale_x_discrete’ dice_plot_4: no visible global function definition for ‘scale_y_discrete’ dice_plot_4: no visible global function definition for ‘theme’ dice_plot_4: no visible global function definition for ‘element_text’ dice_plot_4: no visible global function definition for ‘element_blank’ dice_plot_4: no visible global function definition for ‘unit’ dice_plot_4: no visible global function definition for ‘labs’ dice_plot_4: no visible global function definition for ‘coord_fixed’ dice_plot_4: no visible global function definition for ‘ggtitle’ dice_plot_4: no visible global function definition for ‘guides’ dice_plot_4: no visible binding for global variable ‘x’ dice_plot_4: no visible binding for global variable ‘y’ dice_plot_4: no visible binding for global variable ‘var’ dice_plot_4: no visible global function definition for ‘theme_void’ dice_plot_4: no visible global function definition for ‘margin’ dice_plot_4: no visible global function definition for ‘coord_cartesian’ dice_plot_4: no visible global function definition for ‘geom_text’ dice_plot_4: no visible global function definition for ‘ggdraw’ dice_plot_4: no visible global function definition for ‘draw_plot’ dice_plot_4: no visible global function definition for ‘ggsave’ dice_plot_5: no visible global function definition for ‘theme_minimal’ dice_plot_5: no visible global function definition for ‘%>%’ dice_plot_5: no visible global function definition for ‘group_by’ dice_plot_5: no visible global function definition for ‘sym’ dice_plot_5: no visible global function definition for ‘summarise’ dice_plot_5: no visible global function definition for ‘n_distinct’ dice_plot_5: no visible global function definition for ‘filter’ dice_plot_5: no visible binding for global variable ‘unique_groups’ dice_plot_5: no visible global function definition for ‘ggplot’ dice_plot_5: no visible global function definition for ‘geom_rect’ dice_plot_5: no visible global function definition for ‘aes’ dice_plot_5: no visible binding for global variable ‘x_min’ dice_plot_5: no visible binding for global variable ‘x_max’ dice_plot_5: no visible binding for global variable ‘y_min’ dice_plot_5: no visible binding for global variable ‘y_max’ dice_plot_5: no visible global function definition for ‘geom_point’ dice_plot_5: no visible binding for global variable ‘x_pos’ dice_plot_5: no visible binding for global variable ‘y_pos’ dice_plot_5: no visible global function definition for ‘scale_color_manual’ dice_plot_5: no visible global function definition for ‘scale_fill_manual’ dice_plot_5: no visible global function definition for ‘scale_x_discrete’ dice_plot_5: no visible global function definition for ‘scale_y_discrete’ dice_plot_5: no visible global function definition for ‘theme’ dice_plot_5: no visible global function definition for ‘element_text’ dice_plot_5: no visible global function definition for ‘element_blank’ dice_plot_5: no visible global function definition for ‘unit’ dice_plot_5: no visible global function definition for ‘labs’ dice_plot_5: no visible global function definition for ‘coord_fixed’ dice_plot_5: no visible global function definition for ‘ggtitle’ dice_plot_5: no visible global function definition for ‘guides’ dice_plot_5: no visible global function definition for ‘mutate’ dice_plot_5: no visible binding for global variable ‘x_offset’ dice_plot_5: no visible binding for global variable ‘y_offset’ dice_plot_5: no visible binding for global variable ‘x’ dice_plot_5: no visible binding for global variable ‘y’ dice_plot_5: no visible binding for global variable ‘var’ dice_plot_5: no visible global function definition for ‘theme_void’ dice_plot_5: no visible global function definition for ‘margin’ dice_plot_5: no visible global function definition for ‘coord_cartesian’ dice_plot_5: no visible global function definition for ‘geom_text’ dice_plot_5: no visible global function definition for ‘ggdraw’ dice_plot_5: no visible global function definition for ‘draw_plot’ dice_plot_5: no visible global function definition for ‘ggsave’ dice_plot_6: no visible global function definition for ‘theme_minimal’ dice_plot_6: no visible global function definition for ‘%>%’ dice_plot_6: no visible global function definition for ‘group_by’ dice_plot_6: no visible global function definition for ‘sym’ dice_plot_6: no visible global function definition for ‘summarise’ dice_plot_6: no visible global function definition for ‘n_distinct’ dice_plot_6: no visible global function definition for ‘filter’ dice_plot_6: no visible binding for global variable ‘unique_groups’ dice_plot_6: no visible global function definition for ‘ggplot’ dice_plot_6: no visible global function definition for ‘geom_rect’ dice_plot_6: no visible global function definition for ‘aes’ dice_plot_6: no visible binding for global variable ‘x_min’ dice_plot_6: no visible binding for global variable ‘x_max’ dice_plot_6: no visible binding for global variable ‘y_min’ dice_plot_6: no visible binding for global variable ‘y_max’ dice_plot_6: no visible global function definition for ‘geom_point’ dice_plot_6: no visible binding for global variable ‘x_pos’ dice_plot_6: no visible binding for global variable ‘y_pos’ dice_plot_6: no visible global function definition for ‘scale_color_manual’ dice_plot_6: no visible global function definition for ‘scale_fill_manual’ dice_plot_6: no visible global function definition for ‘scale_x_discrete’ dice_plot_6: no visible global function definition for ‘scale_y_discrete’ dice_plot_6: no visible global function definition for ‘theme’ dice_plot_6: no visible global function definition for ‘element_text’ dice_plot_6: no visible global function definition for ‘element_blank’ dice_plot_6: no visible global function definition for ‘unit’ dice_plot_6: no visible global function definition for ‘labs’ dice_plot_6: no visible global function definition for ‘coord_fixed’ dice_plot_6: no visible global function definition for ‘ggtitle’ dice_plot_6: no visible global function definition for ‘guides’ dice_plot_6: no visible global function definition for ‘mutate’ dice_plot_6: no visible binding for global variable ‘x_offset’ dice_plot_6: no visible binding for global variable ‘y_offset’ dice_plot_6: no visible binding for global variable ‘x’ dice_plot_6: no visible binding for global variable ‘y’ dice_plot_6: no visible binding for global variable ‘var’ dice_plot_6: no visible global function definition for ‘theme_void’ dice_plot_6: no visible global function definition for ‘margin’ dice_plot_6: no visible global function definition for ‘coord_cartesian’ dice_plot_6: no visible global function definition for ‘geom_text’ dice_plot_6: no visible global function definition for ‘ggdraw’ dice_plot_6: no visible global function definition for ‘draw_plot’ dice_plot_6: no visible global function definition for ‘ggsave’ domino_plot: no visible global function definition for ‘%>%’ domino_plot: no visible binding for global variable ‘gene’ domino_plot: no visible global function definition for ‘select’ domino_plot: no visible binding for global variable ‘var’ domino_plot: no visible binding for global variable ‘Contrast’ domino_plot: no visible global function definition for ‘distinct’ domino_plot: no visible global function definition for ‘mutate’ domino_plot: no visible binding for global variable ‘Celltype’ domino_plot: no visible binding for global variable ‘y_offset’ domino_plot: no visible binding for global variable ‘avg_log2FC’ domino_plot: no visible binding for global variable ‘p_val_adj’ domino_plot: no visible global function definition for ‘ggplot’ domino_plot: no visible global function definition for ‘aes’ domino_plot: no visible binding for global variable ‘x_pos’ domino_plot: no visible binding for global variable ‘y_pos’ domino_plot: no visible global function definition for ‘geom_rect’ domino_plot: no visible global function definition for ‘geom_point’ domino_plot: no visible binding for global variable ‘log_p_val_adj’ domino_plot: no visible global function definition for ‘scale_color_gradient2’ domino_plot: no visible global function definition for ‘scale_size_continuous’ domino_plot: no visible global function definition for ‘scale_x_continuous’ domino_plot: no visible global function definition for ‘expansion’ domino_plot: no visible global function definition for ‘scale_y_continuous’ domino_plot: no visible global function definition for ‘labs’ domino_plot: no visible global function definition for ‘theme_minimal’ domino_plot: no visible global function definition for ‘theme’ domino_plot: no visible global function definition for ‘element_text’ domino_plot: no visible global function definition for ‘element_line’ domino_plot: no visible global function definition for ‘element_blank’ domino_plot: no visible global function definition for ‘element_rect’ domino_plot: no visible global function definition for ‘annotate’ domino_plot: no visible global function definition for ‘coord_flip’ domino_plot: no visible global function definition for ‘coord_cartesian’ domino_plot: no visible global function definition for ‘ggsave’ order_cat_b: no visible global function definition for ‘%>%’ order_cat_b: no visible global function definition for ‘mutate’ order_cat_b: no visible global function definition for ‘:=’ order_cat_b: no visible global function definition for ‘sym’ order_cat_b: no visible global function definition for ‘group_by’ order_cat_b: no visible global function definition for ‘summarise’ order_cat_b: no visible global function definition for ‘n’ order_cat_b: no visible global function definition for ‘arrange’ order_cat_b: no visible global function definition for ‘desc’ order_cat_b: no visible binding for global variable ‘count’ order_cat_b: no visible global function definition for ‘pull’ perform_clustering: no visible global function definition for ‘%>%’ perform_clustering: no visible global function definition for ‘mutate’ perform_clustering: no visible global function definition for ‘group_by’ perform_clustering: no visible global function definition for ‘sym’ perform_clustering: no visible global function definition for ‘summarise’ perform_clustering: no visible binding for global variable ‘present’ perform_clustering: no visible global function definition for ‘unite’ perform_clustering: no visible global function definition for ‘pivot_wider’ perform_clustering: no visible binding for global variable ‘combined’ perform_clustering: no visible binding for global variable ‘value’ perform_clustering: no visible global function definition for ‘column_to_rownames’ perform_clustering: no visible global function definition for ‘dist’ perform_clustering: no visible global function definition for ‘hclust’ prepare_box_data: no visible global function definition for ‘%>%’ prepare_box_data: no visible global function definition for ‘mutate’ prepare_box_data: no visible global function definition for ‘:=’ prepare_box_data: no visible global function definition for ‘sym’ prepare_box_data: no visible global function definition for ‘distinct’ prepare_box_data: no visible global function definition for ‘arrange’ prepare_plot_data: no visible global function definition for ‘%>%’ prepare_plot_data: no visible global function definition for ‘left_join’ prepare_plot_data: no visible global function definition for ‘setNames’ prepare_plot_data: no visible global function definition for ‘mutate’ prepare_plot_data: no visible global function definition for ‘:=’ prepare_plot_data: no visible global function definition for ‘sym’ prepare_plot_data: no visible binding for global variable ‘x_offset’ prepare_plot_data: no visible binding for global variable ‘y_offset’ prepare_plot_data: no visible global function definition for ‘arrange’ Undefined global functions or variables: %>% := Celltype Contrast aes annotate arrange avg_log2FC column_to_rownames combined coord_cartesian coord_fixed coord_flip count desc dist distinct draw_plot element_blank element_line element_rect element_text expansion filter gene geom_point geom_rect geom_text ggdraw ggplot ggsave ggtitle group_by guides hclust labs left_join log_p_val_adj margin mutate n n_distinct p_val_adj pivot_wider present pull scale_color_gradient2 scale_color_manual scale_fill_manual scale_size_continuous scale_x_continuous scale_x_discrete scale_y_continuous scale_y_discrete select setNames summarise sym theme theme_minimal theme_void unique_groups unit unite value var x x_max x_min x_offset x_pos y y_max y_min y_offset y_pos Consider adding importFrom("stats", "dist", "filter", "hclust", "setNames", "var") to your NAMESPACE file. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘dice_plot’ ‘domino_plot’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... WARNING 'library' or 'require' call not declared from: ‘tibble’ * checking tests ... [6s/6s] OK Running ‘test_diceplots.R’ [4s/4s] Running ‘test_domino_base.R’ [2s/2s] * checking PDF version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 2 NOTEs