* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EMTscore.Rcheck’ * using R Under development (unstable) (2025-04-10 r88129) * 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) Omics (3:53) mesenchymal (7:25) omics (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. Size of tarball: 8062986 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 ... 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 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 ‘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 ‘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 sdE sdM stat_density2d summarise text_grob theme theme_void unit * 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 ... OK * checking for code/documentation mismatches ... OK * 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 ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [43s/43s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed Execute_multiple_plot 23.342 0.615 23.964 * checking PDF version of manual ... [3s/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: 3 NOTEs