* using log directory 'd:/RCompile/CRANincoming/R-devel/tSNEr.Rcheck' * using R Under development (unstable) (2025-11-16 r89026 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'tSNEr/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tSNEr' version '1.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Chen Liu ' New submission Possibly misspelled words in DESCRIPTION: Cytometry (3:44) FCS (13:20) SNE (3:22, 12:70) cytometry (13:10) Unknown, possibly misspelled, fields in DESCRIPTION: 'Remotes' Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/base64enc/index.html From: README.md Status: 200 Message: OK CRAN URL not in canonical form The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'tSNEr' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE 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: 'Chen LIu [aut]' Authors@R: 'Chen Liu [aut] (ORCID: )' Maintainer field differs from that derived from Authors@R Maintainer: 'Chen Liu ' Authors@R: '' * checking top-level files ... NOTE Non-standard file/directory found at top level: 'LICENSE.md' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... WARNING Found the following file with non-ASCII characters: R/functions.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function 'tools::showNonASCIIfile' can help in finding non-ASCII characters in files. * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: 'jsonlite' 'knitr' 'scales' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE confirm_file_groups: no visible global function definition for 'setNames' create_combined_plots: no visible global function definition for 'txtProgressBar' create_combined_plots: no visible global function definition for 'setTxtProgressBar' create_combined_plots: no visible global function definition for 'ggplot' create_combined_plots: no visible global function definition for 'aes' create_combined_plots: no visible binding for global variable 'tSNE_1' create_combined_plots: no visible binding for global variable 'tSNE_2' create_combined_plots: no visible binding for global variable '.data' create_combined_plots: no visible global function definition for 'geom_point' create_combined_plots: no visible global function definition for 'scale_color_viridis_c' create_combined_plots: no visible global function definition for 'coord_fixed' create_combined_plots: no visible global function definition for 'theme_minimal' create_combined_plots: no visible global function definition for 'theme' create_combined_plots: no visible global function definition for 'element_text' create_combined_plots: no visible global function definition for 'unit' create_combined_plots: no visible global function definition for 'margin' create_combined_plots: no visible global function definition for 'element_rect' create_combined_plots: no visible global function definition for 'element_line' create_combined_plots: no visible global function definition for 'element_blank' create_combined_plots: no visible global function definition for 'labs' create_combined_plots: no visible global function definition for 'guides' create_combined_plots: no visible global function definition for 'guide_colorbar' create_combined_plots: no visible global function definition for 'ggsave' create_visualisation_plots: no visible global function definition for 'quantile' create_visualisation_plots: no visible global function definition for 'ggplot' create_visualisation_plots: no visible global function definition for 'aes' create_visualisation_plots: no visible binding for global variable 'tSNE1' create_visualisation_plots: no visible binding for global variable 'tSNE2' create_visualisation_plots: no visible binding for global variable '.data' create_visualisation_plots: no visible global function definition for 'geom_point' create_visualisation_plots: no visible global function definition for 'scale_color_gradientn' create_visualisation_plots: no visible global function definition for 'labs' create_visualisation_plots: no visible global function definition for 'coord_fixed' create_visualisation_plots: no visible global function definition for 'theme_minimal' create_visualisation_plots: no visible global function definition for 'theme' create_visualisation_plots: no visible global function definition for 'element_text' create_visualisation_plots: no visible global function definition for 'margin' create_visualisation_plots: no visible global function definition for 'ggsave' generate_custom_pdf: no visible global function definition for 'pdf' generate_custom_pdf: no visible global function definition for 'dev.off' load_multiple_fcs: no visible global function definition for 'read.FCS' load_multiple_fcs: no visible global function definition for 'exprs' main: no visible global function definition for 'write.csv' run_tsne_analysis: no visible global function definition for 'Rtsne' Undefined global functions or variables: .data Rtsne aes coord_fixed dev.off element_blank element_line element_rect element_text exprs geom_point ggplot ggsave guide_colorbar guides labs margin pdf quantile read.FCS scale_color_gradientn scale_color_viridis_c setNames setTxtProgressBar tSNE1 tSNE2 tSNE_1 tSNE_2 theme theme_minimal txtProgressBar unit write.csv Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "quantile", "setNames") importFrom("utils", "setTxtProgressBar", "txtProgressBar", "write.csv") to your NAMESPACE file. * checking for missing documentation entries ... WARNING Undocumented code objects: 'confirm_file_groups' 'create_combined_plots' 'create_visualisation_plots' 'downsample_data' 'find_and_select_multiple_fcs' 'generate_custom_pdf' 'generate_html_report' 'get_tsne_params' 'load_multiple_fcs' 'main' 'result' 'run_tsne_analysis' 'select_markers' 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 PDF version of manual ... OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * DONE Status: 4 WARNINGs, 4 NOTEs