* using log directory 'd:/RCompile/CRANincoming/R-devel/GPEMR.Rcheck' * using R Under development (unstable) (2024-08-15 r87022 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'GPEMR/DESCRIPTION' ... OK * this is package 'GPEMR' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Ruqaiya Shaikh ' New submission Possibly misspelled words in DESCRIPTION: Bertalanffy (8:173) GPEM (8:417) GPEMR (8:19) Gompertz (8:190) Von (8:169) The Description field contains App](https://gpem-r.shinyapps.io/GPEM-R/). Please enclose URLs in angle brackets (<...>). * 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 ... WARNING Found the following file with a non-portable file name: MIT License These are not fully portable file names. See section 'Package structure' in the 'Writing R Extensions' manual. * checking whether package 'GPEMR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT License * checking top-level files ... NOTE Non-standard file/directory found at top level: 'MIT License' * 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 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 comparison_plot: no visible global function definition for 'read.table' comparison_plot: no visible global function definition for 'read.csv' comparison_plot: no visible global function definition for 'lines' comparison_plot: no visible global function definition for 'legend' comparison_plot: no visible global function definition for 'abline' p_value_calc: no visible global function definition for 'read.table' p_value_calc: no visible global function definition for 'read.csv' p_value_calc: no visible global function definition for 'optim' p_value_calc: no visible global function definition for 'sd' p_value_calc: no visible global function definition for 'pnorm' real_data: no visible global function definition for 'read.table' real_data: no visible global function definition for 'read.csv' real_data: no visible global function definition for 'optim' real_data: no visible global function definition for 'pnorm' real_data: no visible global function definition for 'par' real_data: no visible global function definition for 'points' real_data: no visible global function definition for 'segments' real_data: no visible global function definition for 'abline' simulated_function: no visible global function definition for 'optim' simulated_function: no visible global function definition for 'par' Undefined global functions or variables: abline legend lines optim par pnorm points read.csv read.table sd segments Consider adding importFrom("graphics", "abline", "legend", "lines", "par", "points", "segments") importFrom("stats", "optim", "pnorm", "sd") importFrom("utils", "read.csv", "read.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'comparison_plot.Rd': \examples lines wider than 100 characters: comparison_plot(data_path = "data.csv", window_size = 5, parameter = params, p_val_method = "Parametric", repetition = 10) Rd file 'real_data.Rd': \examples lines wider than 100 characters: results_logistic <- real_data("data.txt", window_size = 5, model = "Logistic", parameter = parameter_logistic, cov = TRUE, Plot_est = T ... [TRUNCATED] results_gompertz <- real_data("data.csv", window_size = 5, model = "Gompertz", parameter = parameter_gompertz, cov = FALSE, Plot_est = ... [TRUNCATED] Rd file 'simulated_function.Rd': \examples lines wider than 100 characters: res <- simulated_function(time_points, n, window_size, model, parameter, sigma2, rho, x_0, cov = TRUE, Plot_est = TRUE) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'p_value_calc.Rd' 'data_path' 'window_size' 'model' 'parameter' 'p_val_method' 'repetition' 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... NOTE Files named as vignettes but with no recognized vignette engine: 'vignettes/README.Rmd' (Is a VignetteBuilder field missing?) * checking examples ... ERROR Running examples in 'GPEMR-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: comparison_plot > ### Title: Comparison Plot for p-values Across Growth Models > ### Aliases: comparison_plot > > ### ** Examples > > # Define parameters > params <- list(log_r = 0.7, von_r = 0.2,b = 0.3,c = 0.1) > > # Generate comparison plot for p-values using specified data and settings > comparison_plot(data_path = "data.csv", window_size = 5, parameter = params, p_val_method = "Parametric", repetition = 10) Warning in file(file, "rt") : cannot open file 'data.csv': No such file or directory Error in file(file, "rt") : cannot open the connection Calls: comparison_plot -> as.matrix -> read.csv -> read.table -> file Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [177s] OK Running 'testthat.R' [177s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 6 NOTEs