############################################################################## ############################################################################## ### ### 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_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck’ * using R version 4.5.2 Patched (2025-11-04 r88984) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.8 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BindingSiteFinder’ version ‘2.8.0’ * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BSFind.Rd: GenomicRanges, CompressedGRangesList annotateWithScore.Rd: GenomicRanges assignToGenes.Rd: GenomicRanges, overlaps assignToTranscriptRegions.Rd: CompressedGRangesList, overlaps bindingSiteDefinednessPlot.Rd: ggplot calculateBsBackground.Rd: GenomicRanges duplicatedSitesPlot.Rd: ggplot estimateBsWidth.Rd: GenomicRanges estimateBsWidthPlot.Rd: ggplot geneOverlapsPlot.Rd: ggplot geneRegulationPlot.Rd: GenomicRanges globalScorePlot.Rd: ggplot makeBsSummaryPlot.Rd: ggplot mergeCrosslinkDiagnosticsPlot.Rd: ggplot plotBsBackgroundFilter.Rd: ggplot plotBsMA.Rd: ggplot plotBsVolcano.Rd: ggplot processingStepsFlowChart.Rd: ggplot pureClipGeneWiseFilter.Rd: GenomicRanges, overlaps pureClipGlobalFilter.Rd: GenomicRanges pureClipGlobalFilterPlot.Rd: ggplot reproducibilityFilterPlot.Rd: ggplot reproducibilitySamplesPlot.Rd: ggplot targetGeneSpectrumPlot.Rd: ggplot transcriptRegionOverlapsPlot.Rd: ggplot transcriptRegionSpectrumPlot.Rd: ggplot Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 37.541 0.411 60.261 BSFind 32.359 0.447 51.379 processingStepsFlowChart 31.686 0.398 50.736 bindingSiteDefinednessPlot 30.365 0.549 45.306 calculateBsFoldChange 22.819 0.339 36.130 plotBsMA 15.567 0.176 24.621 plotBsVolcano 14.339 0.187 22.586 geneRegulationPlot 13.846 0.158 22.089 bindingSiteCoveragePlot 13.303 0.379 19.260 estimateBsWidthPlot 11.277 0.193 18.095 estimateBsWidth 10.685 0.183 16.783 rangeCoveragePlot 8.899 0.168 14.088 calculateBsBackground 7.407 0.091 11.618 plotBsBackgroundFilter 6.190 0.119 10.138 reproducibilityScatterPlot 5.959 0.077 8.899 mergeSummaryPlot 4.983 0.071 8.129 supportRatioPlot 4.479 0.060 7.650 filterBsBackground 4.172 0.074 6.620 supportRatio 4.051 0.061 6.465 combineBSF 3.596 0.081 5.875 calculateSignalToFlankScore 3.572 0.052 5.726 reproducibilityCutoffPlot 3.510 0.041 5.454 makeBsSummaryPlot 3.419 0.057 5.661 geneOverlapsPlot 3.315 0.072 5.317 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck/00check.log’ for details.