############################################################################## ############################################################################## ### ### 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_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BindingSiteFinder’ version ‘2.2.0’ * 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 ‘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 77.146 0.748 82.918 processingStepsFlowChart 65.026 4.495 92.461 bindingSiteDefinednessPlot 66.405 1.211 73.915 BSFind 64.937 0.873 71.183 calculateBsFoldChange 41.611 0.549 79.453 plotBsMA 27.348 0.429 29.731 plotBsVolcano 26.020 0.403 27.528 estimateBsWidth 20.432 3.264 52.067 estimateBsWidthPlot 20.753 1.578 41.008 bindingSiteCoveragePlot 17.286 0.606 20.097 calculateBsBackground 13.680 0.121 14.784 rangeCoveragePlot 13.363 0.157 14.406 mergeSummaryPlot 10.906 2.453 15.117 plotBsBackgroundFilter 11.597 0.344 12.947 filterBsBackground 9.228 0.220 10.139 reproducibilityScatterPlot 9.052 0.094 9.777 supportRatioPlot 8.640 0.078 9.114 supportRatio 8.173 0.073 8.649 reproducibilityCutoffPlot 7.586 0.245 8.561 geneOverlapsPlot 7.364 0.206 10.747 combineBSF 7.088 0.226 13.991 transcriptRegionOverlapsPlot 6.539 0.045 7.003 transcriptRegionSpectrumPlot 6.472 0.069 6.902 assignToTranscriptRegions 6.129 0.057 6.577 makeBindingSites 6.095 0.081 6.623 imputeBsDifferencesForTestdata 5.871 0.071 6.368 targetGeneSpectrumPlot 5.804 0.049 6.201 assignToGenes 5.360 0.050 6.142 add-BSFDataSet 5.072 0.082 5.399 reproducibilityFilterPlot 4.944 0.045 5.630 clipCoverage 3.654 0.069 6.944 calculateSignalToFlankScore 2.772 0.073 5.216 coverageOverRanges 2.438 0.135 5.382 * 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