* using log directory ‘/srv/hornik/tmp/CRAN_pretest/DRtool.Rcheck’ * using R Under development (unstable) (2025-09-04 r88794) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘DRtool/DESCRIPTION’ ... OK * this is package ‘DRtool’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Justin Lin ’ New submission Unknown, possibly misspelled, fields in DESCRIPTION: ‘Remotes’ Found the following (possibly) invalid URLs: URL: https://rdcu.be/edjyF (moved to https://www.nature.com/articles/doi:10.1038/nbt.4314.epdf?sharing_token=G7k__zflxFlYhRLIRySpAtRgN0jAjWel9jnR3ZoTv0NFmV-pW0O8ddmuAfWKT7uTCry4tCzWyL3Wzdfnz5B_0wyyWhwrSsy-9fWd7f0j5VlMUrbzKpcqFWIoL27QL8fWgCGw_KLJuImgYWttt7L_PQ%3D%3D) From: man/Wong_high.Rd Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. Size of tarball: 5219851 bytes Found the following URLs which should use \doi (with the DOI name only): File ‘Wong_high.Rd’: https://doi.org/10.1016/j.immuni.2016.07.007 * 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 ‘DRtool’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... 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 add_path: no visible binding for global variable ‘x’ add_path: no visible binding for global variable ‘y’ get_projection_inner: no visible global function definition for ‘prcomp’ get_projection_inner: no visible global function definition for ‘predict’ get_projection_inner: no visible global function definition for ‘capture.output’ get_sim_param: no visible global function definition for ‘prcomp’ meta_data_plot: no visible binding for global variable ‘group’ meta_data_plot: no visible binding for global variable ‘data’ meta_data_plot_brush: no visible binding for global variable ‘group’ meta_data_plot_brush: no visible binding for global variable ‘data’ mst_test: no visible global function definition for ‘sd’ mst_test_brush: no visible global function definition for ‘sd’ plot_2d_projection: no visible binding for global variable ‘x’ plot_2d_projection: no visible binding for global variable ‘y’ plot_2d_projection: no visible binding for global variable ‘color’ plot_2d_projection: no visible binding for global variable ‘xend’ plot_2d_projection: no visible binding for global variable ‘yend’ plot_2d_projection_brush: no visible binding for global variable ‘x’ plot_2d_projection_brush: no visible binding for global variable ‘y’ plot_2d_projection_brush: no visible binding for global variable ‘color’ plot_2d_projection_brush: no visible binding for global variable ‘xend’ plot_2d_projection_brush: no visible binding for global variable ‘yend’ plot_heatmap: no visible global function definition for ‘hclust’ plot_heatmap: no visible global function definition for ‘dist’ plot_heatmap: no visible global function definition for ‘as.dendrogram’ plot_heatmap: no visible global function definition for ‘reorder’ plot_heatmap_brush: no visible global function definition for ‘hclust’ plot_heatmap_brush: no visible global function definition for ‘dist’ plot_heatmap_brush: no visible global function definition for ‘as.dendrogram’ plot_heatmap_brush: no visible global function definition for ‘reorder’ run_app: no visible global function definition for ‘dist’ run_app: no visible binding for global variable ‘x’ run_app: no visible binding for global variable ‘y’ run_app : server: no visible binding for global variable ‘x’ run_app : server: no visible binding for global variable ‘y’ run_app : server: no visible binding for global variable ‘.’ run_example: no visible binding for global variable ‘MNIST_pca’ run_example: no visible binding for global variable ‘MNIST_low’ run_example: no visible binding for global variable ‘MNIST_labels’ run_example: no visible binding for global variable ‘MNIST_id’ run_example: no visible binding for global variable ‘MNIST_kmeans_cluster’ run_example: no visible binding for global variable ‘Wong_high’ run_example: no visible binding for global variable ‘Wong_low’ run_example: no visible binding for global variable ‘Wong_organ_labels’ run_example: no visible binding for global variable ‘Wong_cell_labels’ run_example: no visible binding for global variable ‘Wong_kmeans’ sim_crossings_inner : : no visible global function definition for ‘runif’ sim_crossings_inner : : no visible global function definition for ‘dist’ sim_crossings_inner: no visible global function definition for ‘runif’ sim_crossings_inner: no visible global function definition for ‘dist’ Undefined global functions or variables: . MNIST_id MNIST_kmeans_cluster MNIST_labels MNIST_low MNIST_pca Wong_cell_labels Wong_high Wong_kmeans Wong_low Wong_organ_labels as.dendrogram capture.output color data dist group hclust prcomp predict reorder runif sd x xend y yend Consider adding importFrom("stats", "as.dendrogram", "dist", "hclust", "prcomp", "predict", "reorder", "runif", "sd") importFrom("utils", "capture.output", "data") to your NAMESPACE file. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [0s/0s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [17s/19s] 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: 2 NOTEs