############################################################################## ############################################################################## ### ### 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_2.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BindingSiteFinder.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 ‘2.3.1’ * 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 quickFigure 76.245 0.601 82.914 bindingSiteDefinednessPlot 65.782 2.435 131.176 processingStepsFlowChart 65.671 0.925 71.511 BSFind 65.022 0.858 71.395 calculateBsFoldChange 40.405 2.349 73.634 plotBsVolcano 27.454 5.790 46.938 plotBsMA 28.564 0.895 32.195 estimateBsWidth 21.303 2.641 27.098 estimateBsWidthPlot 22.000 0.529 24.184 bindingSiteCoveragePlot 17.289 0.589 20.210 calculateBsBackground 12.558 2.589 34.270 rangeCoveragePlot 14.590 0.175 15.348 plotBsBackgroundFilter 11.759 0.303 13.556 mergeSummaryPlot 9.435 0.137 10.415 filterBsBackground 9.105 0.186 10.085 reproducibilityScatterPlot 8.965 0.076 9.568 supportRatioPlot 8.583 0.063 9.156 supportRatio 8.346 0.071 9.085 combineBSF 7.056 0.158 7.590 geneOverlapsPlot 6.994 0.158 8.577 transcriptRegionSpectrumPlot 6.749 0.165 9.036 transcriptRegionOverlapsPlot 6.551 0.080 7.392 reproducibilityCutoffPlot 6.232 0.045 6.993 assignToTranscriptRegions 5.999 0.051 6.299 makeBindingSites 5.930 0.092 6.564 imputeBsDifferencesForTestdata 5.610 0.081 6.168 targetGeneSpectrumPlot 5.644 0.036 5.957 assignToGenes 5.252 0.040 5.660 add-BSFDataSet 5.029 0.065 5.277 reproducibilityFilterPlot 4.890 0.150 5.345 calculateSignalToFlankScore 3.668 0.664 5.456 * 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