* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EMTscore.Rcheck’ * using R Under development (unstable) (2025-04-08 r88126) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘EMTscore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EMTscore’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘haimei wen ’ New submission Possibly misspelled words in DESCRIPTION: EMTscore (7:1051, 7:1495) mesenchymal (7:25) omics (3:53, 7:611, 7:1325, 7:1588) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Haimei", family = "Wen", role = c("aut", "cre"), email = "hudie.luoluo@gmail.com"), person(given = "Daniel", family = "Lopez", role = "aut"), person(given = "Tian", family = "Hong", role = "aut")) as necessary. The Title field should be in title case. Current version is: ‘A toolbox for scoring multi-context EMT from omics data’ In title case that is: ‘A Toolbox for Scoring Multi-Context EMT from Omics Data’ Size of tarball: 14157914 bytes * 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 ‘EMTscore’ can be installed ... [10s/10s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘figure’ * 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 ... [2s/2s] NOTE AUCellfunc: no visible global function definition for ‘AUCell_buildRankings’ AUCellfunc: no visible global function definition for ‘AUCell_calcAUC’ AUCellfunc: no visible global function definition for ‘getAUC’ Execute_E_M_plot: no visible global function definition for ‘ggplot’ Execute_E_M_plot: no visible global function definition for ‘aes’ Execute_E_M_plot: no visible binding for global variable ‘Escore’ Execute_E_M_plot: no visible binding for global variable ‘Mscore’ Execute_E_M_plot: no visible binding for global variable ‘celltype_annotation’ Execute_E_M_plot: no visible global function definition for ‘geom_point’ Execute_E_M_plot: no visible global function definition for ‘scale_colour_manual’ Execute_E_M_plot: no visible global function definition for ‘stat_density2d’ Execute_E_M_plot: no visible global function definition for ‘%>%’ Execute_E_M_plot: no visible global function definition for ‘group_by’ Execute_E_M_plot: no visible global function definition for ‘summarise’ Execute_E_M_plot: no visible global function definition for ‘n’ Execute_E_M_plot: no visible global function definition for ‘sd’ Execute_E_M_plot: no visible global function definition for ‘geom_errorbar’ Execute_E_M_plot: no visible binding for global variable ‘mE’ Execute_E_M_plot: no visible binding for global variable ‘mM’ Execute_E_M_plot: no visible binding for global variable ‘sdM’ Execute_E_M_plot: no visible global function definition for ‘geom_errorbarh’ Execute_E_M_plot: no visible binding for global variable ‘sdE’ Execute_E_M_plot: no visible global function definition for ‘scale_fill_manual’ Execute_E_M_plot: no visible global function definition for ‘theme’ Execute_E_M_plot: no visible global function definition for ‘element_rect’ Execute_E_M_plot: no visible global function definition for ‘element_text’ Execute_E_M_plot: no visible global function definition for ‘unit’ Execute_E_M_plot: no visible global function definition for ‘element_blank’ Execute_M_dimension_plot: no visible global function definition for ‘ggplot’ Execute_M_dimension_plot: no visible global function definition for ‘aes’ Execute_M_dimension_plot: no visible binding for global variable ‘M1_score’ Execute_M_dimension_plot: no visible binding for global variable ‘M2_score’ Execute_M_dimension_plot: no visible binding for global variable ‘celltype_annotation’ Execute_M_dimension_plot: no visible global function definition for ‘geom_point’ Execute_M_dimension_plot: no visible global function definition for ‘scale_colour_manual’ Execute_M_dimension_plot: no visible global function definition for ‘stat_density2d’ Execute_M_dimension_plot: no visible global function definition for ‘%>%’ Execute_M_dimension_plot: no visible global function definition for ‘group_by’ Execute_M_dimension_plot: no visible global function definition for ‘summarise’ Execute_M_dimension_plot: no visible global function definition for ‘n’ Execute_M_dimension_plot: no visible global function definition for ‘sd’ Execute_M_dimension_plot: no visible global function definition for ‘geom_errorbar’ Execute_M_dimension_plot: no visible binding for global variable ‘mE’ Execute_M_dimension_plot: no visible binding for global variable ‘mM’ Execute_M_dimension_plot: no visible binding for global variable ‘sdM’ Execute_M_dimension_plot: no visible global function definition for ‘geom_errorbarh’ Execute_M_dimension_plot: no visible binding for global variable ‘sdE’ Execute_M_dimension_plot: no visible global function definition for ‘scale_fill_manual’ Execute_M_dimension_plot: no visible global function definition for ‘theme’ Execute_M_dimension_plot: no visible global function definition for ‘element_rect’ Execute_M_dimension_plot: no visible global function definition for ‘element_text’ Execute_M_dimension_plot: no visible global function definition for ‘unit’ Execute_M_dimension_plot: no visible global function definition for ‘element_blank’ Execute_multiple_plot: no visible global function definition for ‘annotate_figure’ Execute_multiple_plot: no visible global function definition for ‘ggarrange’ Execute_multiple_plot: no visible global function definition for ‘text_grob’ Execute_multiple_plot : : no visible global function definition for ‘ggplot’ Execute_multiple_plot : : no visible global function definition for ‘ggtitle’ Execute_multiple_plot : : no visible global function definition for ‘theme_void’ Execute_multiple_plot : : no visible global function definition for ‘theme’ Execute_multiple_plot : : no visible global function definition for ‘element_text’ Execute_nnPCA: no visible global function definition for ‘nsprcomp’ Execute_nnPCA_plot: no visible global function definition for ‘ggtitle’ Execute_nnPCA_plot: no visible global function definition for ‘annotate_figure’ Execute_nnPCA_plot: no visible global function definition for ‘ggarrange’ Execute_nnPCA_plot: no visible global function definition for ‘text_grob’ Execute_ssGSEA: no visible global function definition for ‘gsvaParam’ Execute_ssGSEA: no visible global function definition for ‘gsva’ plot_heatmap_function: no visible global function definition for ‘nsprcomp’ plot_heatmap_function: no visible global function definition for ‘colorRamp2’ plot_heatmap_function: no visible global function definition for ‘rowAnnotation’ plot_heatmap_function: no visible global function definition for ‘HeatmapAnnotation’ plot_heatmap_function: no visible global function definition for ‘Heatmap’ Undefined global functions or variables: %>% AUCell_buildRankings AUCell_calcAUC Escore Heatmap HeatmapAnnotation M1_score M2_score Mscore aes annotate_figure celltype_annotation colorRamp2 element_blank element_rect element_text geom_errorbar geom_errorbarh geom_point getAUC ggarrange ggplot ggtitle group_by gsva gsvaParam mE mM n nsprcomp rowAnnotation scale_colour_manual scale_fill_manual sd sdE sdM stat_density2d summarise text_grob theme theme_void unit Consider adding importFrom("stats", "sd") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'Execute_E_M_plot.Rd': \examples lines wider than 100 characters: Execute_E_M_plot(cell_annotation_file, Methods, geneExp, M_signature_gene_sets = Panchy_et_al_M_signature, E_signature_gene_sets = Panc ... [TRUNCATED] Rd file 'Execute_M_dimension_plot.Rd': \examples lines wider than 100 characters: Execute_M_dimension_plot(cell_annotation_file ,geneExp, M_signature_gene_sets = Panchy_et_al_M_signature) # only for nnPCA method Rd file 'Execute_multiple_plot.Rd': \examples lines wider than 100 characters: gene_lists <- list(Panchy_et_al = list(Panchy_et_al_M_signature, Panchy_et_al_E_signature), Tan_et_al_tumor = list(Tan_et_al_tumor_M_si ... [TRUNCATED] Execute_multiple_plot( geneExp, cell_annotation_file, method, gene_lists, fig_title = 'RPM') # only for nnPCA method Rd file 'Execute_nnPCA.Rd': \examples lines wider than 100 characters: nnPCA_Mscore <- Execute_nnPCA(geneExp, Panchy_et_al_M_signature, dimension=2,score_names=c('M1_score','M2_score')) Rd file 'Execute_nnPCA_plot.Rd': \examples lines wider than 100 characters: gene_lists <- list(Panchy_et_al = list(Panchy_et_al_M_signature, Panchy_et_al_E_signature), Tan_et_al_tumor = list(Tan_et_al_tumor_M_si ... [TRUNCATED] Execute_nnPCA_plot(cell_annotation_file, geneExp, gene_lists, fig_title = 'RPM') # only for nnPCA method These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘AUCellfunc’ ‘stringsAsFactors’ 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 ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'Execute_AUCell.Rd' ‘colnames’ Documented arguments not in \usage in Rd file 'Execute_M_dimension_plot.Rd': ‘E_signature_gene_sets’ Undocumented arguments in Rd file 'Execute_SCSE.Rd' ‘colnames’ Documented arguments not in \usage in Rd file 'Execute_multiple_plot.Rd': ‘M_signature_gene_sets’ ‘E_signature_gene_sets’ Undocumented arguments in Rd file 'Execute_nnPCA.Rd' ‘dimension’ ‘score_names’ Documented arguments not in \usage in Rd file 'Execute_nnPCA_plot.Rd': ‘M_signature_gene_sets’ ‘E_signature_gene_sets’ Undocumented arguments in Rd file 'Execute_ssGSEA.Rd' ‘colnames’ Undocumented arguments in Rd file 'SingleCellSigExplorer.Rd' ‘data’ ‘genes’ Undocumented arguments in Rd file 'plot_heatmap_function.Rd' ‘geneList_M’ Documented arguments not in \usage in Rd file 'plot_heatmap_function.Rd': ‘cell_annotation_file’ ‘method’ ‘M_signature_gene_sets’ ‘E_signature_gene_sets’ ‘gene_lists’ ‘fig_title’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING 'library' or 'require' call not declared from: ‘gridExtra’ * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... WARNING LazyData DB of 13.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress geneExp.rda 13.1Mb 7.7Mb xz * checking examples ... [41s/41s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed Execute_multiple_plot 23.08 0.635 23.723 * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 5 WARNINGs, 5 NOTEs