############################################################################## ############################################################################## ### ### 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 4.4.2 (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 76.070 0.523 79.084 processingStepsFlowChart 64.950 0.741 68.942 BSFind 62.211 0.723 73.402 bindingSiteDefinednessPlot 58.306 2.589 109.894 calculateBsFoldChange 43.539 3.067 50.864 plotBsMA 28.949 3.164 38.188 plotBsVolcano 26.365 0.219 27.108 estimateBsWidth 21.231 0.426 22.286 estimateBsWidthPlot 19.957 0.346 20.679 bindingSiteCoveragePlot 16.075 0.714 31.008 plotBsBackgroundFilter 12.205 2.436 18.195 rangeCoveragePlot 13.142 0.139 14.298 calculateBsBackground 11.704 0.328 13.068 mergeSummaryPlot 9.295 0.087 10.219 filterBsBackground 8.655 0.090 8.828 reproducibilityScatterPlot 8.624 0.050 8.875 supportRatioPlot 8.520 0.062 8.725 supportRatio 8.170 0.203 8.491 geneOverlapsPlot 6.865 0.108 7.418 combineBSF 6.870 0.101 7.218 transcriptRegionSpectrumPlot 6.506 0.067 7.133 transcriptRegionOverlapsPlot 6.466 0.036 6.747 assignToTranscriptRegions 6.116 0.045 12.170 makeBindingSites 6.048 0.053 6.554 reproducibilityCutoffPlot 6.042 0.054 6.363 imputeBsDifferencesForTestdata 5.756 0.059 6.485 targetGeneSpectrumPlot 5.641 0.038 5.889 assignToGenes 5.262 0.054 10.229 add-BSFDataSet 5.078 0.058 10.879 annotateWithScore 3.641 0.029 7.009 * 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