* using log directory ‘/srv/hornik/tmp/CRAN/GPEMR.Rcheck’
* using R Under development (unstable) (2024-08-15 r87022)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* 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 ... [3s/4s] NOTE
Maintainer: ‘Ruqaiya Shaikh <ruqaiyashaikh41@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  Bertalanffy (8:173)
  GPEM (8:417)
  GPEMR (8:19)
  Gompertz (8:190)
  Von (8:169)

Found the following (possibly) invalid URLs:
  URL: https://gpem-r.shinyapps.io/GPEM-R/
    From: DESCRIPTION
    Status: 202
    Message: Accepted

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 executable files ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GPEMR’ can be installed ... [2s/2s] 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 ... [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 ... [4s/4s] 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 ... [0s/0s] 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 ... [0s/0s] 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 ... [162s/162s] OK
  Running ‘testthat.R’ [162s/162s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 6 NOTEs