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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:XAItest.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings XAItest_1.1.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/XAItest.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘XAItest/DESCRIPTION’ ... OK
* this is package ‘XAItest’ version ‘1.1.5’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘XAItest’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 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 ... NOTE
genScenario : <anonymous>: no visible global function definition for
  ‘runif’
genScenario: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘addSimThresh’ ‘genScenario’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'XAI.test.Rd':
XAI.test
  Code: function(data, y = "y", featImpAgr = "mean", simData = FALSE,
                 simMethod = "regrnorm", simPvalTarget = 0.045,
                 adjMethod = "bonferroni", customPVals = NULL,
                 customFeatImps = NULL, customFIPV = NULL, modelType =
                 "default", corMethod = "pearson", defaultMethods =
                 c("ttest", "ebayes", "cor", "lm", "rf", "shap",
                 "lime"), caretMethod = "rf", caretTrainArgs = NULL,
                 verbose = FALSE)
  Docs: function(data, y = "y", featImpAgr = "mean", simData = FALSE,
                 simMethod = "regrnorm", simPvalTarget = 0.045,
                 adjMethod = "bonferroni", customPVals = NULL,
                 customFeatImps = NULL, modelType = "default",
                 corMethod = "pearson", defaultMethods = c("ttest",
                 "ebayes", "cor", "lm", "rf", "shap", "lime"),
                 caretMethod = "rf", caretTrainArgs = NULL, verbose =
                 FALSE)
  Argument names in code not in docs:
    customFIPV
  Mismatches in argument names (first 3):
    Position: 10 Code: customFIPV Docs: modelType
    Position: 11 Code: modelType Docs: corMethod
    Position: 12 Code: corMethod Docs: defaultMethods

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
XAI.test       36.427  0.846  35.603
modelsOverview 35.877  0.263  34.479
plotModel      11.561  0.085  11.017
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/XAItest.Rcheck/00check.log’
for details.