* using log directory 'd:/RCompile/CRANincoming/R-devel/PKbioanalysis.Rcheck'
* using R Under development (unstable) (2026-01-08 r89292 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'PKbioanalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PKbioanalysis' version '0.4.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] NOTE
Maintainer: 'Omar Elashkar <omar.i.elashkar@gmail.com>'

Found the following (possibly) invalid URLs:
  URL: https://github.com/OmarAshkar/PKbioanalysis/actions/workflows/R-CMD-check.yaml
    From: README.md
    Status: 404
    Message: Not Found
  URL: https://github.com/OmarAshkar/PKbioanalysis/issues
    From: DESCRIPTION
          man/PKbioanalysis-package.Rd
    Status: 404
    Message: Not Found
* 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 'PKbioanalysis' 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 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 ... NOTE
Warning in readLines(file, warn = readLines.warn) :
  incomplete final line found on 'C:\Users\CRAN\AppData\Roaming/R/config/R/PKbioanalysis/config.yaml'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [45s] OK
* 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 ... [13s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [81s] ERROR
  Running 'testthat.R' [81s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PKbioanalysis)
  
  Attaching package: 'PKbioanalysis'
  
  The following object is masked from 'package:stats':
  
      integrate
  
  Warning message:
  In readLines(file, warn = readLines.warn) :
    incomplete final line found on 'C:\Users\CRAN\AppData\Roaming/R/config/R/PKbioanalysis/config.yaml'
  > 
  > test_check("PKbioanalysis")
  
  ── Reading Waters Raw Files 
  ℹ Found 7 raw files
  → Loading
  Error in `chr()`:
  ! Can't splice S3 objects
  Backtrace:
       ▆
    1. ├─testthat::test_check("PKbioanalysis")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─PKbioanalysis::read_chrom(path, method = 1) at ./helper-global.R:23:1
   15. │                         └─PKbioanalysis:::.parsewatersraw(dir)
   16. │                           └─base::lapply(x, function(x) rawreadr(x))
   17. │                             └─PKbioanalysis (local) FUN(X[[i]], ...)
   18. │                               └─PKbioanalysis (local) rawreadr(x)
   19. │                                 ├─py$masslynx_parser
   20. │                                 └─reticulate:::`$.python.builtin.module`(py, "masslynx_parser")
   21. │                                   └─reticulate::py_get_attr(x, name, FALSE)
   22. ├─base::stop(`<python.builtin.AttributeError>`)
   23. ├─testthat (local) `<fn>`(`<python.builtin.AttributeError>`)
   24. │ └─cli::cli_abort(...)
   25. │   └─rlang::abort(...)
   26. │     └─rlang:::signal_abort(cnd, .file)
   27. │       └─rlang::cnd_message(cnd, inherit = TRUE, prefix = TRUE)
   28. │         └─rlang:::format_onerror_backtrace(orig, opt = backtrace_on_error)
   29. │           └─rlang:::paste_line(...)
   30. │             └─rlang::chr(...)
   31. └─rlang::abort(message = message)
  Execution halted
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [13s] OK
* DONE
Status: 1 ERROR, 2 NOTEs