############################################################################## ############################################################################## ### ### Running command: ### ### /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 ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BindingSiteFinder.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 74.201 0.466 76.643 processingStepsFlowChart 64.564 0.652 66.429 bindingSiteDefinednessPlot 62.962 1.497 69.788 BSFind 62.451 1.380 123.678 calculateBsFoldChange 42.314 2.697 48.349 plotBsMA 27.432 0.223 28.410 estimateBsWidthPlot 22.184 4.474 33.422 plotBsVolcano 25.816 0.212 28.402 estimateBsWidth 20.744 0.724 22.403 bindingSiteCoveragePlot 16.614 2.990 34.668 rangeCoveragePlot 13.174 0.250 13.548 calculateBsBackground 11.570 0.307 12.796 filterBsBackground 9.746 1.966 16.438 plotBsBackgroundFilter 11.310 0.204 11.883 mergeSummaryPlot 9.135 0.177 9.396 reproducibilityScatterPlot 8.867 0.066 9.965 supportRatioPlot 8.468 0.051 8.556 geneOverlapsPlot 7.349 0.865 10.328 supportRatio 8.151 0.059 8.596 reproducibilityCutoffPlot 7.494 0.084 7.708 combineBSF 6.870 0.135 7.343 transcriptRegionOverlapsPlot 6.448 0.032 6.535 transcriptRegionSpectrumPlot 6.367 0.038 6.766 makeBindingSites 5.880 0.040 5.985 imputeBsDifferencesForTestdata 5.683 0.046 5.805 targetGeneSpectrumPlot 5.500 0.030 5.648 assignToTranscriptRegions 5.065 0.142 9.294 add-BSFDataSet 4.879 0.162 9.233 reproducibilityFilterPlot 4.903 0.094 5.554 assignToGenes 4.501 0.124 7.823 * 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