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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_2.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.3.1’
* 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
BSFind                        36.564  0.561  37.478
quickFigure                   35.224  1.392  65.809
processingStepsFlowChart      33.331  2.727  41.198
bindingSiteDefinednessPlot    34.630  0.627  41.811
calculateBsFoldChange         21.150  0.823  39.429
plotBsMA                      12.388  0.604  15.022
plotBsVolcano                 12.105  0.317  13.349
estimateBsWidth               10.137  1.400  22.407
bindingSiteCoveragePlot       10.244  0.449  10.792
estimateBsWidthPlot           10.119  0.541  25.352
rangeCoveragePlot              7.561  0.600  13.174
calculateBsBackground          6.898  0.091   9.785
plotBsBackgroundFilter         4.984  0.438  11.575
mergeSummaryPlot               4.319  0.531  10.756
combineBSF                     3.962  0.148   7.012
filterBsBackground             3.814  0.258  12.162
makeBindingSites               2.725  0.255  12.485
makeBsSummaryPlot              1.536  0.224   8.947
mergeCrosslinkDiagnosticsPlot  1.514  0.153   7.460
* 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