* using log directory 'd:/RCompile/CRANincoming/R-devel/MetAlyzer.Rcheck'
* using R Under development (unstable) (2024-10-30 r87277 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 'MetAlyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetAlyzer' version '1.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [16s] NOTE
Maintainer: 'Nils Mechtel <nils.mech@gmail.com>'

Found the following (possibly) invalid URLs:
  URL: https://cran.r-project.org/web/packages/MetAlyzer/vignettes/MetAlyzer_User_Guide.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
The canonical URL of the CRAN page for a package is 
  https://CRAN.R-project.org/package=pkgname
* 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 'build' directory ... 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 ... 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 ... [41s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'summarizeConcValues.Rd':
  \examples lines wider than 100 characters:
     metalyzer_se <- MetAlyzer_dataset(file_path = "/Users/larrylusi/Downloads/2024-09-10_DISC_THRX_Tissue+TRP.xlsx")

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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [93s] ERROR
Running examples in 'MetAlyzer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summarizeConcValues
> ### Title: Summarize concentration values
> ### Aliases: summarizeConcValues
> 
> ### ** Examples
> 
> metalyzer_se <- MetAlyzer_dataset(file_path = example_extraction_data())


 _____ ______   _______  _________  ________  ___           ___    ___ ________  _______   ________
|\   _ \  _   \|\  ___ \|\___   ___\\   __  \|\  \         |\  \  /  /|\_____  \|\  ___ \ |\   __  \
\ \  \\\__\ \  \ \   __/\|___ \  \_\ \  \|\  \ \  \        \ \  \/  / /\|___/  /\ \   __/|\ \  \|\  \
 \ \  \\|__| \  \ \  \_|/__  \ \  \ \ \   __  \ \  \        \ \    / /     /  / /\ \  \_|/_\ \   _  _\
  \ \  \    \ \  \ \  \_|\ \  \ \  \ \ \  \ \  \ \  \____    \/   / /     /  /_/__\ \  \_|\ \ \  \\  \| 
   \ \__\    \ \__\ \_______\  \ \__\ \ \__\ \__\ \_______\__/   / /     |\________\ \_______\ \__\\ _\ 
    \|__|     \|__|\|_______|   \|__|  \|__|\|__|\|_______|\____/ /       \|_______|\|_______|\|__|\|__|
                                                          \|____|/


Info: Reading color code "FFFFCCCC" as "#FFCCCC"
Info: Reading color code "FF00CD66" as "#00CD66"
Info: Reading color code "FF6A5ACD" as "#6A5ACD"
Info: Reading color code "FF87CEEB" as "#87CEEB"
Info: Reading color code "FFFFFFCC" as "#FFFFCC"

Measured concentration values:
------------------------------
        0%        25%        50%        75%       100% 
     0.000      0.017      1.760     21.200 288149.000 

NAs: 5348 (8.38%)
Note: 'Metabolism Indicators' are frequently NA!

Measured quantification status:
-------------------------------
Valid: 24095 (37.77%)
LOQ: 5799 (9.09%)
LOD: 21789 (34.16%)
Invalid: 12105 (18.98%)
NAs: 0 (0%)

> metalyzer_se <- MetAlyzer_dataset(file_path = "/Users/larrylusi/Downloads/2024-09-10_DISC_THRX_Tissue+TRP.xlsx")


 _____ ______   _______  _________  ________  ___           ___    ___ ________  _______   ________
|\   _ \  _   \|\  ___ \|\___   ___\\   __  \|\  \         |\  \  /  /|\_____  \|\  ___ \ |\   __  \
\ \  \\\__\ \  \ \   __/\|___ \  \_\ \  \|\  \ \  \        \ \  \/  / /\|___/  /\ \   __/|\ \  \|\  \
 \ \  \\|__| \  \ \  \_|/__  \ \  \ \ \   __  \ \  \        \ \    / /     /  / /\ \  \_|/_\ \   _  _\
  \ \  \    \ \  \ \  \_|\ \  \ \  \ \ \  \ \  \ \  \____    \/   / /     /  /_/__\ \  \_|\ \ \  \\  \| 
   \ \__\    \ \__\ \_______\  \ \__\ \ \__\ \__\ \_______\__/   / /     |\________\ \_______\ \__\\ _\ 
    \|__|     \|__|\|_______|   \|__|  \|__|\|__|\|_______|\____/ /       \|_______|\|_______|\|__|\|__|
                                                          \|____|/


Error in read.xlsx.default(starter_list$file_path, sheet = starter_list$sheet,  : 
  File does not exist.
Calls: MetAlyzer_dataset -> open_file -> <Anonymous> -> read.xlsx.default
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [239s] OK
* checking PDF version of manual ... [29s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs