* using log directory 'd:/RCompile/CRANincoming/R-devel/FAST.R.Rcheck' * using R Under development (unstable) (2023-12-09 r85665 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'FAST.R/DESCRIPTION' ... OK * this is package 'FAST.R' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Francesco Neri ' New submission Found the following (possibly) invalid URLs: URL: https://github.com/f-neri/FAST-R_2.0/actions/workflows/R-CMD-check.yaml (moved to https://github.com/f-neri/FAST.R/actions/workflows/R-CMD-check.yaml) From: README.md 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. * 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 serialization versions ... OK * checking whether package 'FAST.R' can be installed ... OK * checking installed package size ... 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 R 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 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 ... NOTE analyze_single_cell_data: no visible binding for global variable 'EdU' analyze_single_cell_data: no visible binding for global variable 'SABGal' analyze_single_cell_data: no visible binding for global variable 'Nuclear_Area' analyze_single_cell_data: no visible binding for global variable 'EdU_threshold' analyze_single_cell_data: no visible binding for global variable 'SABGal_threshold' analyze_single_cell_data: no visible binding for global variable 'counts_EdU_positive' analyze_single_cell_data: no visible binding for global variable 'cell_counts' analyze_single_cell_data: no visible binding for global variable 'counts_SABGal_positive' analyze_single_cell_data: no visible binding for global variable 'counts_EdU_negative_SABGal_negative' analyze_single_cell_data: no visible binding for global variable 'counts_EdU_negative_SABGal_positive' analyze_single_cell_data: no visible binding for global variable 'counts_EdU_positive_SABGal_negative' analyze_single_cell_data: no visible binding for global variable 'counts_EdU_positive_SABGal_positive' analyze_single_cell_data: no visible binding for global variable 'Nuclear_Area_median' analyze_single_cell_data: no visible binding for global variable 'EdU_median' analyze_single_cell_data: no visible binding for global variable 'SABGal_median' analyze_single_cell_data: no visible binding for global variable 'Nuclear_Area_median_reference' analyze_single_cell_data: no visible binding for global variable 'EdU_median_reference' analyze_single_cell_data: no visible binding for global variable 'SABGal_median_reference' analyze_single_cell_data: no visible binding for global variable 'Condition' analyze_single_cell_data: no visible binding for global variable 'plate' analyze_single_cell_data: no visible binding for global variable 'well' analyze_single_cell_data: no visible global function definition for 'everything' data_analysisServer : : no visible binding for global variable '.' data_analysisServer : : no visible binding for global variable 'IAoutput_name' data_analysisServer : : no visible binding for global variable 'metadata_name' data_analysisServer : : no visible binding for global variable 'plate' data_analysisServer : : no visible binding for global variable 'well' data_analysisServer : : no visible binding for global variable 'cell_ID' data_visualizationServer : : no visible binding for global variable 'Condition' data_visualizationServer : : no visible binding for global variable 'SABGal' data_visualizationServer : : no visible binding for global variable 'EdU' data_visualizationServer : : no visible binding for global variable 'SABGal_threshold_average' data_visualizationServer : : no visible binding for global variable 'EdU_threshold_average' data_visualizationServer : : no visible binding for global variable 'value' generate_df_thresholds: no visible binding for global variable 'plate' generate_df_thresholds: no visible binding for global variable 'EdU_threshold' generate_df_thresholds: no visible binding for global variable 'SABGal_threshold' generate_example_single_cell_data : generate_plate_data: no visible binding for global variable 'Condition' get_dim: no visible binding for global variable '.' plot_median_SABGal_EdU_staining: no visible binding for global variable 'SABGal_median' plot_median_SABGal_EdU_staining: no visible binding for global variable 'EdU_median' plot_median_SABGal_EdU_staining: no visible binding for global variable 'Condition' plot_median_SABGal_EdU_staining: no visible binding for global variable 'SABGal_threshold_average_log10' plot_median_SABGal_EdU_staining: no visible binding for global variable 'EdU_threshold_average_log10' plot_median_SABGal_EdU_staining_comparison: no visible binding for global variable 'SABGal_median' plot_median_SABGal_EdU_staining_comparison: no visible binding for global variable 'EdU_median' plot_median_SABGal_EdU_staining_comparison: no visible binding for global variable 'Condition' plot_percentages: no visible binding for global variable 'Condition' plot_percentages: no visible binding for global variable 'Positivity' plot_percentages: no visible binding for global variable 'Percentage' plot_single_cell_SABGal_EdU_staining: no visible binding for global variable 'SABGal_log10' plot_single_cell_SABGal_EdU_staining: no visible binding for global variable 'EdU_log10' plot_single_cell_SABGal_EdU_staining: no visible binding for global variable 'Condition' plot_single_cell_SABGal_EdU_staining: no visible binding for global variable 'SABGal_threshold_average_log10' plot_single_cell_SABGal_EdU_staining: no visible binding for global variable 'EdU_threshold_average_log10' plot_well_percentages: no visible binding for global variable 'percentage_SABGal_positive' plot_well_percentages: no visible binding for global variable 'percentage_EdU_positive' plot_well_percentages: no visible binding for global variable 'Condition' plot_well_percentages_comparison: no visible binding for global variable 'percentage_SABGal_positive' plot_well_percentages_comparison: no visible binding for global variable 'percentage_EdU_positive' plot_well_percentages_comparison: no visible binding for global variable 'Condition' rearrange_df_columns: no visible global function definition for 'everything' tidy_IAoutput: no visible binding for global variable 'Name' tidy_IAoutput: no visible global function definition for 'all_of' tidy_IAoutput: no visible binding for global variable 'Channel' tidy_IAoutput: no visible binding for global variable 'well' tidy_IAoutput: no visible binding for global variable 'cell_ID' tidy_IAoutput: no visible global function definition for 'everything' tidy_IAoutput: no visible binding for global variable 'Measured_Parameter' tidy_IAoutput: no visible binding for global variable 'Signal_Intensity' Undefined global functions or variables: . Channel Condition EdU EdU_log10 EdU_median EdU_median_reference EdU_threshold EdU_threshold_average EdU_threshold_average_log10 IAoutput_name Measured_Parameter Name Nuclear_Area Nuclear_Area_median Nuclear_Area_median_reference Percentage Positivity SABGal SABGal_log10 SABGal_median SABGal_median_reference SABGal_threshold SABGal_threshold_average SABGal_threshold_average_log10 Signal_Intensity all_of cell_ID cell_counts counts_EdU_negative_SABGal_negative counts_EdU_negative_SABGal_positive counts_EdU_positive counts_EdU_positive_SABGal_negative counts_EdU_positive_SABGal_positive counts_SABGal_positive everything metadata_name percentage_EdU_positive percentage_SABGal_positive plate value well * 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 examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking PDF version of manual ... [17s] OK * checking HTML version of manual ... OK * DONE Status: 2 NOTEs