* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SpaCCI.Rcheck’ * using R Under development (unstable) (2024-09-02 r87090) * 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 ‘SpaCCI/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpaCCI’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Li-Ting Ku ’ New submission Possibly misspelled words in DESCRIPTION: CellChat (11:234) CellPhoneDB (11:244) Cellinker (11:257) ConnectomeDB (11:282) ICELLNET (11:268) ligand (11:83, 11:307) transcriptomics (11:181) * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SpaCCI’ can be installed ... [20s/20s] OK * used C++ compiler: ‘Debian clang version 18.1.8 (9)’ * checking package directory ... OK * checking for future file timestamps ... 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [3s/3s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [3s/3s] 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 ... [15s/15s] NOTE SpaCCI_global: no visible global function definition for ‘txtProgressBar’ SpaCCI_global: no visible global function definition for ‘setTxtProgressBar’ SpaCCI_global: no visible global function definition for ‘p.adjust’ SpaCCI_local: no visible global function definition for ‘txtProgressBar’ SpaCCI_local: no visible global function definition for ‘setTxtProgressBar’ SpaCCI_local: no visible global function definition for ‘p.adjust’ SpaCCI_region: no visible global function definition for ‘txtProgressBar’ SpaCCI_region: no visible global function definition for ‘setTxtProgressBar’ SpaCCI_region: no visible global function definition for ‘p.adjust’ plot_SpaCCI_chordDiagram: no visible global function definition for ‘%>%’ plot_SpaCCI_chordDiagram: no visible binding for global variable ‘significant’ plot_SpaCCI_chordDiagram: no visible binding for global variable ‘Cell_type_Ligand’ plot_SpaCCI_chordDiagram: no visible binding for global variable ‘Cell_type_Receptor’ plot_SpaCCI_chordDiagram: no visible global function definition for ‘n’ plot_SpaCCI_chordDiagram: no visible global function definition for ‘strwidth’ plot_SpaCCI_heatmap: no visible global function definition for ‘%>%’ plot_SpaCCI_heatmap: no visible binding for global variable ‘significant’ plot_SpaCCI_heatmap: no visible binding for global variable ‘Cell_type_Ligand’ plot_SpaCCI_heatmap: no visible binding for global variable ‘Cell_type_Receptor’ plot_SpaCCI_heatmap: no visible global function definition for ‘n’ plot_localized: no visible global function definition for ‘ggplot’ plot_localized: no visible global function definition for ‘aes’ plot_localized: no visible binding for global variable ‘imagecol’ plot_localized: no visible binding for global variable ‘imagerow’ plot_localized: no visible binding for global variable ‘CCIcount’ plot_localized: no visible global function definition for ‘geom_point’ plot_localized: no visible global function definition for ‘scale_color_gradient2’ plot_localized: no visible global function definition for ‘labs’ plot_localized: no visible global function definition for ‘xlim’ plot_localized: no visible global function definition for ‘ylim’ plot_localized: no visible global function definition for ‘theme’ plot_localized: no visible global function definition for ‘margin’ plot_localized: no visible global function definition for ‘element_rect’ plot_localized: no visible global function definition for ‘element_blank’ plot_localized: no visible global function definition for ‘element_text’ plot_localized: no visible global function definition for ‘unit’ possible_L_R_pairs_Cellinker: no visible global function definition for ‘read.delim’ possible_L_R_pairs_Cellinker: no visible global function definition for ‘%>%’ possible_L_R_pairs_Cellinker: no visible global function definition for ‘rename’ possible_L_R_pairs_Cellinker: no visible binding for global variable ‘KEGG.pathway’ possible_L_R_pairs_ICELLNET: no visible global function definition for ‘read.csv’ possible_L_R_pairs_cellchat: no visible binding for global variable ‘CellChatDB_human’ possible_L_R_pairs_cellchat: no visible binding for global variable ‘CellChatDB_mouse’ possible_L_R_pairs_cellphoneDB: no visible global function definition for ‘read.csv’ possible_L_R_pairs_cellphoneDB: no visible global function definition for ‘%>%’ possible_L_R_pairs_cellphoneDB: no visible global function definition for ‘rename’ possible_L_R_pairs_cellphoneDB: no visible binding for global variable ‘interactors’ possible_L_R_pairs_cellphoneDB: no visible binding for global variable ‘classification’ possible_L_R_pairs_connectome: no visible binding for global variable ‘LR_pairs_ConnectomeDB_2020’ random_region: no visible global function definition for ‘%>%’ random_region: no visible global function definition for ‘arrange’ random_region: no visible binding for global variable ‘Distance’ random_region: no visible global function definition for ‘head’ Undefined global functions or variables: %>% CCIcount CellChatDB_human CellChatDB_mouse Cell_type_Ligand Cell_type_Receptor Distance KEGG.pathway LR_pairs_ConnectomeDB_2020 aes arrange classification element_blank element_rect element_text geom_point ggplot head imagecol imagerow interactors labs margin n p.adjust read.csv read.delim rename scale_color_gradient2 setTxtProgressBar significant strwidth theme txtProgressBar unit xlim ylim Consider adding importFrom("graphics", "strwidth") importFrom("stats", "p.adjust") importFrom("utils", "head", "read.csv", "read.delim", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'LR_database.Rd': \examples lines wider than 100 characters: rownames(gene_spot_expression_dataframe) <- paste0("Gene", 1:100) # should match the Human or Mouse gene symbol name result <- LR_database(species = "Human", database_name = "CellChat", gene_spot_expression_dataframe = gene_spot_expression_dataframe) Rd file 'possible_L_R_pairs_Cellinker.Rd': \examples lines wider than 100 characters: gene_spot_expression_dataframe = gene_spot_expression_dataframe) gene_spot_expression_dataframe = gene_spot_expression_dataframe) Rd file 'possible_L_R_pairs_ICELLNET.Rd': \examples lines wider than 100 characters: result <- possible_L_R_pairs_ICELLNET(gene_spot_expression_dataframe = gene_spot_expression_dataframe) Rd file 'possible_L_R_pairs_cellphoneDB.Rd': \examples lines wider than 100 characters: result <- possible_L_R_pairs_cellphoneDB(gene_spot_expression_dataframe = gene_spot_expression_dataframe) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... NOTE Auto-generated content requiring editing in Rd file 'SpaCCI-package.Rd': \references: ‘This optional section can contain literature or other refere...’ \seealso: ‘Optional links to other man pages’ \examples: ‘\dontrun{ ## Optional simple examples of the most impor...’ * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [7s/7s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 NOTEs