* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SQUIRE.Rcheck’
* using R Under development (unstable) (2025-11-09 r88992)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (7)
    Debian flang-new version 19.1.7 (7)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘SQUIRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SQUIRE’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Richard A. Feiss <feiss026@umn.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  MNPRO (12:1176)
  al (12:409)
  et (12:406)
  gatekeeping (12:1096)

Found the following (possibly) invalid URLs:
  URL: https://github.com/richardfeiss/SQUIRE/actions
    From: README.md
    Status: 404
    Message: Not Found
  URL: https://github.com/richardfeiss/SQUIRE/issues
    From: README.md
    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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SQUIRE’ can be installed ... [1s/1s] 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 ... [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 ... WARNING
'::' or ':::' import not declared from: ‘numDeriv’
* checking S3 generic/method consistency ... WARNING
summary:
  function(object, ...)
summary.SQUIRE:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
assess_data_quality: no visible global function definition for
  ‘aggregate’
calculate_response_metric: no visible global function definition for
  ‘aggregate’
calibrate_optimization_parameters: no visible global function
  definition for ‘sd’
describe_treatment_effects: no visible global function definition for
  ‘sd’
fit_germination_model: no visible global function definition for
  ‘aggregate’
fit_germination_model: no visible global function definition for
  ‘optim’
test_treatment_effects: no visible global function definition for ‘aov’
validate_optimized_parameters: no visible global function definition
  for ‘aov’
Undefined global functions or variables:
  aggregate aov optim sd
Consider adding
  importFrom("stats", "aggregate", "aov", "optim", "sd")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] WARNING
checkRd: (7) SQUIRE.Rd:84-102: Tag \donttest not recognized
* 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 ... WARNING
Undocumented arguments in Rd file 'assess_data_quality.Rd'
  ‘data’ ‘treatments’ ‘min_timepoints’ ‘min_replicates’

Undocumented arguments in Rd file 'calculate_response_metric.Rd'
  ‘data’

Undocumented arguments in Rd file 'calibrate_galahad_parameters.Rd'
  ‘data’ ‘treatments’ ‘response_type’ ‘validation_results’ ‘verbose’

Undocumented arguments in Rd file 'calibrate_optimization_parameters.Rd'
  ‘data’ ‘geometry_config’

Undocumented arguments in Rd file 'compile_optimization_results.Rd'
  ‘treatment_parameters’ ‘treatments’

Undocumented arguments in Rd file 'describe_treatment_effects.Rd'
  ‘param_values’ ‘param_name’

Undocumented arguments in Rd file 'determine_geometry_partitioning.Rd'
  ‘data’ ‘response_type’

Undocumented arguments in Rd file 'extract_significant_subset.Rd'
  ‘data’ ‘validation_results’

Undocumented arguments in Rd file 'fit_biological_model.Rd'
  ‘data’ ‘response_type’ ‘galahad_config’ ‘verbose’

Undocumented arguments in Rd file 'fit_germination_model.Rd'
  ‘data’ ‘galahad_config’ ‘verbose’

Undocumented arguments in Rd file 'generate_biological_interpretation.Rd'
  ‘optimization_results’ ‘parameter_validation’ ‘response_type’

Undocumented arguments in Rd file 'generate_recommendations.Rd'
  ‘validation_results’ ‘parameter_validation’

Undocumented arguments in Rd file 'get_biological_meaning.Rd'
  ‘param_name’ ‘response_type’

Undocumented arguments in Rd file 'perform_validated_optimization.Rd'
  ‘data’ ‘treatments’ ‘galahad_config’ ‘validation_results’
  ‘response_type’ ‘verbose’

Undocumented arguments in Rd file 'summarize_biological_effects.Rd'
  ‘interpretation’ ‘response_type’

Undocumented arguments in Rd file 'test_treatment_effects.Rd'
  ‘data’ ‘treatments’ ‘alpha’ ‘verbose’

Undocumented arguments in Rd file 'validate_optimized_parameters.Rd'
  ‘optimization_results’ ‘treatments’ ‘control_treatment’ ‘alpha’
  ‘verbose’

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 examples ... NONE
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 5 WARNINGs, 2 NOTEs