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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BindingSiteFinder.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 ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.4.0’
* 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 ‘BindingSiteFinder’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
quickFigure                    74.651  0.448  76.859
processingStepsFlowChart       65.804  2.820  70.993
bindingSiteDefinednessPlot     63.619  3.116 129.553
BSFind                         63.616  0.674  65.527
calculateBsFoldChange          43.463  3.980  54.743
plotBsMA                       28.622  4.617  39.847
plotBsVolcano                  27.168  3.936  37.169
estimateBsWidth                20.541  0.507  22.017
estimateBsWidthPlot            19.962  0.824  22.108
bindingSiteCoveragePlot        16.776  0.557  30.098
calculateBsBackground          11.954  1.782  34.218
rangeCoveragePlot              13.188  0.278  13.739
plotBsBackgroundFilter         11.031  1.182  15.249
filterBsBackground              9.089  0.179  10.302
mergeSummaryPlot                8.766  0.307   9.819
reproducibilityScatterPlot      8.762  0.057   8.893
supportRatioPlot                8.590  0.053   8.739
supportRatio                    7.908  0.044   7.988
combineBSF                      6.917  0.096   7.102
geneOverlapsPlot                6.654  0.161   7.951
transcriptRegionSpectrumPlot    6.453  0.052   6.642
transcriptRegionOverlapsPlot    6.374  0.036   6.452
reproducibilityCutoffPlot       6.094  0.045   6.222
targetGeneSpectrumPlot          5.720  0.119   5.884
assignToTranscriptRegions       5.602  0.050   5.699
imputeBsDifferencesForTestdata  5.475  0.117   5.696
makeBindingSites                5.041  0.060   5.424
add-BSFDataSet                  4.899  0.060   5.043
* 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: OK