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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DegCre.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DegCre_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DegCre.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DegCre/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DegCre’ version ‘1.2.0’
* 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 ‘DegCre’ 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 ... 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 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
calcPadjsAndEtpFun: multiple local function definitions for ‘tpFun’
  with different formal arguments
convDegCreResListToCreGeneScoreGR: no visible global function
  definition for ‘calcAdjAssocProbOR’
Undefined global functions or variables:
  calcAdjAssocProbOR
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'convDegCreResListToCreGeneScoreGR.Rd':
  ‘calcAdjAssocProbOR’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
optimizeAlphaDegCre                21.794  0.508  29.029
plotBrowserDegCre                  21.071  0.705  29.955
degCrePRAUC                        19.002  1.933  26.618
getExpectAssocPerDEG               11.665  0.294  15.249
plotExpectedAssocsPerDeg           11.454  0.123  14.798
calcAssocProbOR                     7.101  0.231   8.917
collapseDegCreToGene                5.868  0.143   7.365
runDegCre                           5.718  0.103   7.361
getDistBinNullAssocProb             5.509  0.148   7.103
convertdegCreResListToGInteraction  4.776  0.078   5.989
convertDegCreDataFrame              4.734  0.100   6.105
convDegCreResListToCreGeneScoreGR   4.657  0.090   5.930
calcRawAssocProbOR                  4.627  0.114   5.868
plotDegCreAssocProbVsDist           4.578  0.076   5.874
plotDegCreBinHeuristic              4.438  0.068   5.974
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/DegCre.Rcheck/00check.log’
for details.