* using log directory 'd:/RCompile/CRANincoming/R-devel/MetAlyzer.Rcheck' * using R Under development (unstable) (2023-11-16 r85542 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 'MetAlyzer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MetAlyzer' version '1.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [10s] NOTE Maintainer: 'Nils Mechtel ' New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: metabolomics (25:78) CRAN repository db overrides: X-CRAN-Comment: Archived on 2023-11-06 as issues were not corrected in time. Package has a VignetteBuilder field but no prebuilt vignette index. * 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 'MetAlyzer' 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 ... NOTE Non-standard file/directory found at top level: 'MetAlyzer.Rproj' * 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 ... [44s] NOTE aggregate_data: no visible binding for global variable 'Metabolite' aggregate_data: no visible binding for global variable 'Concentration' aggregate_data: no visible binding for global variable 'ID' aggregate_data: no visible binding for global variable 'Status' apply_linear_model: no visible binding for global variable 'Value' calc_CV: no visible binding for global variable 'Concentration' calc_CV: no visible binding for global variable 'SD' calc_CV: no visible binding for global variable 'Mean' calc_CV: no visible binding for global variable 'CV' calculate_log2FC: no visible global function definition for ':=' calculate_log2FC: no visible binding for global variable 'ID' calculate_log2FC: no visible binding for global variable 'log2_Conc' calculate_log2FC: no visible binding for global variable 'Metabolite' calculate_log2FC: no visible binding for global variable 'Class' calculate_log2FC: no visible binding for global variable 'Group' calculate_log2FC: no visible binding for global variable 'Value' calculate_log2FC: no visible binding for global variable 'pval' filterMetaData: no visible binding for global variable 'Index' filterMetaData: no visible binding for global variable 'ID' filterMetabolites: no visible global function definition for ':=' filterMetabolites: no visible binding for global variable 'ID' filterMetabolites: no visible binding for global variable 'Status' filterMetabolites: no visible binding for global variable 'Metabolite' filterMetabolites: no visible binding for global variable 'Valid_Group' impute_data: no visible binding for global variable 'Metabolite' impute_data: no visible binding for global variable 'Concentration' plot_log2FC: no visible binding for global variable 'Class' plot_log2FC: no visible binding for global variable 'Polarity' plot_log2FC : : no visible binding for global variable 'Class' plot_log2FC: no visible binding for global variable 'signif_color' plot_log2FC: no visible binding for global variable 'x' plot_log2FC: no visible binding for global variable 'log2FC' plot_log2FC: no visible binding for global variable 'Start' plot_log2FC: no visible binding for global variable 'End' plot_log2FC: no visible binding for global variable 'qval' plot_network: no visible binding for global variable 'Radius' plot_network: no visible binding for global variable 'Color' plot_network: no visible binding for global variable 'x_start' plot_network: no visible binding for global variable 'y_start' plot_network: no visible binding for global variable 'x_end' plot_network: no visible binding for global variable 'y_end' plot_network: no visible binding for global variable 'Node1' plot_network: no visible binding for global variable 'Node2' plot_network: no visible binding for global variable 'x' plot_network: no visible binding for global variable 'y' plot_network: no visible binding for global variable 'Label' plot_network: no visible binding for global variable 'FC_thresh' transform_data: no visible binding for global variable 'imputed_Conc' Undefined global functions or variables: := CV Class Color Concentration End FC_thresh Group ID Index Label Mean Metabolite Node1 Node2 Polarity Radius SD Start Status Valid_Group Value imputed_Conc log2FC log2_Conc pval qval signif_color x x_end x_start y y_end y_start Found if() conditions comparing class() to string: File 'MetAlyzer/R/calculate_log2FC.R': if (class(group_vec) != "factor") ... Use inherits() (or maybe is()) instead. * 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 ... NOTE Documented arguments not in \usage in Rd file 'aggregate_data.Rd': 'meta_columns' Documented arguments not in \usage in Rd file 'open_file.Rd': 'object' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [56s] OK * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 4 NOTEs