############################################################################## ############################################################################## ### ### 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_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘2.1.0’ * 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 R 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 72.957 1.082 93.158 processingStepsFlowChart 64.777 5.361 103.152 BSFind 63.191 1.159 75.506 bindingSiteDefinednessPlot 59.642 1.124 100.476 calculateBsFoldChange 38.475 2.785 90.838 plotBsMA 26.557 0.498 30.140 plotBsVolcano 25.868 0.525 31.632 estimateBsWidthPlot 21.404 0.623 24.435 estimateBsWidth 16.253 3.156 33.120 bindingSiteCoveragePlot 15.737 0.583 25.821 rangeCoveragePlot 13.111 0.447 16.977 plotBsBackgroundFilter 11.325 0.325 13.364 calculateBsBackground 10.651 0.322 21.129 mergeSummaryPlot 9.013 0.149 10.382 filterBsBackground 8.828 0.125 9.585 reproducibilityScatterPlot 8.738 0.179 11.597 supportRatioPlot 8.142 0.177 10.124 supportRatio 8.096 0.146 10.529 combineBSF 6.824 0.183 7.884 geneOverlapsPlot 6.734 0.148 8.112 transcriptRegionSpectrumPlot 6.472 0.162 7.964 transcriptRegionOverlapsPlot 6.464 0.145 8.635 reproducibilityCutoffPlot 6.082 0.148 7.796 targetGeneSpectrumPlot 5.806 0.153 7.861 makeBindingSites 5.759 0.119 6.752 imputeBsDifferencesForTestdata 5.434 0.089 6.159 reproducibilityFilterPlot 4.799 0.097 6.446 clipCoverage 4.280 0.315 10.200 reproducibilitySamplesPlot 4.158 0.073 5.351 add-BSFDataSet 4.093 0.080 5.566 calculateSignalToFlankScore 3.478 0.181 8.514 annotateWithScore 2.987 0.056 7.236 * 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