* using log directory 'd:/RCompile/CRANincoming/R-devel/STEAM.Rcheck' * using R Under development (unstable) (2025-02-02 r87676 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'STEAM/DESCRIPTION' ... OK * this is package 'STEAM' version '1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Revanth Krishna ' New submission Possibly misspelled words in DESCRIPTION: omics (7:78) Unknown, possibly misspelled, fields in DESCRIPTION: 'Correspondance' No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Samantha", family = "Reynoso", role = "aut"), person(given = "Courtney", family = "Schiebout", role = "aut"), person(given = "Revanth", family = "Krishna", role = c("aut", "cre"), email = "revanth.krishna@cuanschutz.edu"), person(given = "Fan", family = "Zhang", role = "aut", comment = "University of Colorado School of Medicine - CU Medicine")) as necessary. Package has a VignetteBuilder field but no prebuilt vignette index. Found the following (possibly) invalid file URIs: URI: link From: README.md URI: fanzhanglab@gmail.com From: README.md The Title field should be in title case. Current version is: 'Training and Evaluating Clustering performance with STEAM' In title case that is: 'Training and Evaluating Clustering Performance with STEAM' Size of tarball: 5903008 bytes * checking package namespace information ... OK * checking package dependencies ... INFO Vignette dependency required without any vignettes: 'knitr' * 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 'STEAM' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE Non-standard files/directories found at top level: 'citations.cff' 'media' 'tutorials' * 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 ... 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 whether startup messages can be suppressed ... 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 ... [12s] NOTE File 'STEAM/R/zzz.R': .onLoad calls: packageStartupMessage("Package: ", desc[, "Package"]) packageStartupMessage("Description: ", desc[, "Description"]) packageStartupMessage("Version: ", desc[, "Version"]) packageStartupMessage("Release Date: ", desc[, "Date"]) packageStartupMessage("Authors: ", desc[, "Author"]) packageStartupMessage("Maintainer: ", desc[, "Maintainer"]) See section 'Good practice' in '?.onAttach'. ViewMetrics : get_text_color: no visible global function definition for 'col2rgb' ViewMetrics: no visible binding for global variable 'Actual_Label' ViewMetrics: no visible binding for global variable 'Predicted_Label' ViewMetrics: no visible binding for global variable 'Value' ViewMetrics: no visible global function definition for 'geom_tile' ViewMetrics: no visible global function definition for 'geom_text' ViewMetrics: no visible binding for global variable 'TextColor' ViewMetrics: no visible global function definition for 'scale_color_identity' ViewMetrics: no visible global function definition for 'theme_classic' ViewMetrics: no visible global function definition for 'element_text' feature_expression: no visible binding for global variable 'Layer' feature_expression: no visible binding for global variable 'Expression' feature_expression: no visible global function definition for 'geom_boxplot' feature_expression: no visible global function definition for 'theme_classic' feature_importance: no visible global function definition for 'coef' feature_importance: no visible global function definition for 'head' feature_importance: no visible global function definition for 'reorder' feature_importance: no visible binding for global variable 'Feature' feature_importance: no visible binding for global variable 'Importance' feature_importance: no visible global function definition for 'geom_bar' feature_importance: no visible global function definition for 'coord_flip' feature_importance: no visible global function definition for 'theme_classic' model.predict: no visible global function definition for 'predict' plot_misclassified_cells : assign_layer_colors: no visible global function definition for 'rainbow' plot_misclassified_cells : assign_layer_colors: no visible global function definition for 'setNames' plot_misclassified_cells: no visible global function definition for 'setNames' plot_misclassified_cells: no visible binding for global variable 'broader_palette' plot_misclassified_cells: no visible binding for global variable 'Col' plot_misclassified_cells: no visible binding for global variable 'Row' plot_misclassified_cells: no visible binding for global variable 'Labels' plot_misclassified_cells: no visible global function definition for 'theme_classic' Undefined global functions or variables: Actual_Label Col Expression Feature Importance Labels Layer Predicted_Label Row TextColor Value broader_palette coef col2rgb coord_flip element_text geom_bar geom_boxplot geom_text geom_tile head predict rainbow reorder scale_color_identity setNames theme_classic Consider adding importFrom("grDevices", "col2rgb", "rainbow") importFrom("stats", "coef", "predict", "reorder", "setNames") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... NONE * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * DONE Status: 1 WARNING, 4 NOTEs