* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PvSTATEM.Rcheck’
* using R Under development (unstable) (2024-09-13 r87144)
* 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 ‘PvSTATEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PvSTATEM’ version ‘0.0.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/8s] NOTE
Maintainer: ‘Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>’

New submission

License components with restrictions and base license permitting such:
  BSD_3_clause + file LICENSE
File 'LICENSE':
  YEAR: 2024
  COPYRIGHT HOLDER: MINI PW

Possibly misspelled words in DESCRIPTION:
  PvSTATEM (9:44)

Found the following (possibly) invalid URLs:
  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5685631/
    From: inst/doc/our_datasets.html
    Status: 403
    Message: Forbidden

The Title field should be in title case. Current version is:
  ‘Reading, quality control and preprocessing of MBA assay data’
In title case that is:
  ‘Reading, Quality Control and Preprocessing of MBA Assay Data’

The Description field should not start with the package name,
  'This package' or similar.
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘PvSTATEM’ can be installed ... [4s/4s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub records with missing/empty fields:
  Record: 1 Field(s): ORGANIZATION
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘dilutions_CovidOISExPONTENT.csv’ ‘pkgdown’
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘verbose_cat’
* checking S3 generic/method consistency ... NOTE
Mismatches for methods registered for non-generic:
predict:
  function(object, ...)
predict.Model:
  function(object, mfi)
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] NOTE
plot_mfi_for_analyte: no visible binding for global variable ‘.’
plot_mfi_for_analyte: no visible binding for global variable
  ‘SampleType’
plot_mfi_for_analyte: no visible binding for global variable ‘MFI’
plot_mfi_for_analyte: no visible binding for global variable ‘SampleId’
plot_mfi_for_analyte: no visible binding for global variable ‘outlier’
plot_plate: no visible global function definition for ‘dev.size’
plot_plate: no visible binding for global variable ‘x’
plot_plate: no visible binding for global variable ‘y’
plot_plate: no visible binding for global variable ‘category’
plot_standard_curve_analyte: no visible binding for global variable
  ‘dilution_values’
plot_standard_curve_analyte: no visible binding for global variable
  ‘MFI’
plot_standard_curve_analyte_with_model: no visible global function
  definition for ‘predict’
plot_standard_curve_analyte_with_model: no visible binding for global
  variable ‘dilution’
plot_standard_curve_analyte_with_model: no visible binding for global
  variable ‘MFI’
process_plate: no visible global function definition for ‘predict’
Undefined global functions or variables:
  . MFI SampleId SampleType category dev.size dilution dilution_values
  outlier predict x y
Consider adding
  importFrom("grDevices", "dev.size")
  importFrom("stats", "predict")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'read_luminex_data.Rd':
  \examples lines wider than 100 characters:
     plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE) # suppress warnings and additional information

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Unknown package ‘pkg’ in Rd xrefs
* 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 ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [6s/6s] OK
  Running ‘testthat.R’ [6s/6s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [29s/29s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘dilutions_CovidOISExPONTENT.csv’
* checking for detritus in the temp directory ... OK
* DONE
Status: 9 NOTEs