############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘singleCellTK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘singleCellTK’ version ‘2.19.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 79 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘singleCellTK’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: extdata 1.5Mb shiny 2.9Mb * 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 whether startup messages can be suppressed ... 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: dedupRowNames.Rd: SingleCellExperiment-class detectCellOutlier.Rd: colData diffAbundanceFET.Rd: colData downSampleCells.Rd: SingleCellExperiment-class downSampleDepth.Rd: SingleCellExperiment-class featureIndex.Rd: SummarizedExperiment-class, SingleCellExperiment-class getBiomarker.Rd: SingleCellExperiment-class getDEGTopTable.Rd: SingleCellExperiment-class getEnrichRResult.Rd: SingleCellExperiment-class getFindMarkerTopTable.Rd: SingleCellExperiment-class getGenesetNamesFromCollection.Rd: SingleCellExperiment-class getPathwayResultNames.Rd: SingleCellExperiment-class getSampleSummaryStatsTable.Rd: SingleCellExperiment-class, assay, colData getSoupX.Rd: SingleCellExperiment-class getTSCANResults.Rd: SingleCellExperiment-class getTopHVG.Rd: SingleCellExperiment-class importAlevin.Rd: DelayedArray, readMM importAnnData.Rd: DelayedArray, readMM importBUStools.Rd: readMM importCellRanger.Rd: readMM, DelayedArray importCellRangerV2Sample.Rd: readMM, DelayedArray importCellRangerV3Sample.Rd: readMM, DelayedArray importDropEst.Rd: DelayedArray, readMM importExampleData.Rd: scRNAseq, Matrix, DelayedArray, ReprocessedFluidigmData, ReprocessedAllenData, NestorowaHSCData importFromFiles.Rd: readMM, DelayedArray, SingleCellExperiment-class importGeneSetsFromCollection.Rd: GeneSetCollection-class, SingleCellExperiment-class, GeneSetCollection, GSEABase, metadata importGeneSetsFromGMT.Rd: GeneSetCollection-class, SingleCellExperiment-class, getGmt, GSEABase, metadata importGeneSetsFromList.Rd: GeneSetCollection-class, SingleCellExperiment-class, GSEABase, metadata importGeneSetsFromMSigDB.Rd: SingleCellExperiment-class, msigdbr, GeneSetCollection-class, GSEABase, metadata importMitoGeneSet.Rd: SingleCellExperiment-class, GeneSetCollection-class, GSEABase, metadata importMultipleSources.Rd: DelayedArray importOptimus.Rd: readMM, DelayedArray importSEQC.Rd: readMM, DelayedArray importSTARsolo.Rd: readMM, DelayedArray iterateSimulations.Rd: SingleCellExperiment-class listSampleSummaryStatsTables.Rd: SingleCellExperiment-class, metadata plotBarcodeRankDropsResults.Rd: SingleCellExperiment-class plotBarcodeRankScatter.Rd: SingleCellExperiment-class plotBatchCorrCompare.Rd: SingleCellExperiment-class plotBatchVariance.Rd: SingleCellExperiment-class plotBcdsResults.Rd: SingleCellExperiment-class plotClusterAbundance.Rd: colData plotCxdsResults.Rd: SingleCellExperiment-class plotDEGHeatmap.Rd: SingleCellExperiment-class plotDEGRegression.Rd: SingleCellExperiment-class plotDEGViolin.Rd: SingleCellExperiment-class plotDEGVolcano.Rd: SingleCellExperiment-class plotDecontXResults.Rd: SingleCellExperiment-class plotDoubletFinderResults.Rd: SingleCellExperiment-class plotEmptyDropsResults.Rd: SingleCellExperiment-class plotEmptyDropsScatter.Rd: SingleCellExperiment-class plotFindMarkerHeatmap.Rd: SingleCellExperiment-class plotPCA.Rd: SingleCellExperiment-class plotPathway.Rd: SingleCellExperiment-class plotRunPerCellQCResults.Rd: SingleCellExperiment-class plotSCEBarAssayData.Rd: SingleCellExperiment-class plotSCEBarColData.Rd: SingleCellExperiment-class plotSCEBatchFeatureMean.Rd: SingleCellExperiment-class plotSCEDensity.Rd: SingleCellExperiment-class plotSCEDensityAssayData.Rd: SingleCellExperiment-class plotSCEDensityColData.Rd: SingleCellExperiment-class plotSCEDimReduceColData.Rd: SingleCellExperiment-class plotSCEDimReduceFeatures.Rd: SingleCellExperiment-class plotSCEHeatmap.Rd: SingleCellExperiment-class plotSCEScatter.Rd: SingleCellExperiment-class plotSCEViolin.Rd: SingleCellExperiment-class plotSCEViolinAssayData.Rd: SingleCellExperiment-class plotSCEViolinColData.Rd: SingleCellExperiment-class plotScDblFinderResults.Rd: SingleCellExperiment-class plotScdsHybridResults.Rd: SingleCellExperiment-class plotScrubletResults.Rd: SingleCellExperiment-class plotSoupXResults.Rd: SingleCellExperiment-class plotTSCANClusterDEG.Rd: SingleCellExperiment-class plotTSCANClusterPseudo.Rd: SingleCellExperiment-class plotTSCANDimReduceFeatures.Rd: SingleCellExperiment-class plotTSCANPseudotimeGenes.Rd: SingleCellExperiment-class plotTSCANPseudotimeHeatmap.Rd: SingleCellExperiment-class plotTSCANResults.Rd: SingleCellExperiment-class plotTSNE.Rd: SingleCellExperiment-class plotUMAP.Rd: SingleCellExperiment-class readSingleCellMatrix.Rd: DelayedArray reportCellQC.Rd: SingleCellExperiment-class reportClusterAbundance.Rd: colData reportDiffAbundanceFET.Rd: colData retrieveSCEIndex.Rd: SingleCellExperiment-class runBBKNN.Rd: SingleCellExperiment-class runBarcodeRankDrops.Rd: SingleCellExperiment-class, colData runBcds.Rd: SingleCellExperiment-class, colData runCellQC.Rd: colData runComBatSeq.Rd: SingleCellExperiment-class runCxds.Rd: SingleCellExperiment-class, colData runCxdsBcdsHybrid.Rd: colData runDEAnalysis.Rd: SingleCellExperiment-class runDecontX.Rd: colData runDimReduce.Rd: SingleCellExperiment-class runDoubletFinder.Rd: SingleCellExperiment-class runDropletQC.Rd: colData runEmptyDrops.Rd: SingleCellExperiment-class, colData runEnrichR.Rd: SingleCellExperiment-class runFastMNN.Rd: SingleCellExperiment-class, BiocParallelParam-class runFeatureSelection.Rd: SingleCellExperiment-class runFindMarker.Rd: SingleCellExperiment-class runGSVA.Rd: SingleCellExperiment-class runHarmony.Rd: SingleCellExperiment-class runKMeans.Rd: SingleCellExperiment-class, colData runLimmaBC.Rd: SingleCellExperiment-class, assay runMNNCorrect.Rd: SingleCellExperiment-class, assay, BiocParallelParam-class runModelGeneVar.Rd: SingleCellExperiment-class runPerCellQC.Rd: SingleCellExperiment-class, BiocParallelParam, colData runSCANORAMA.Rd: SingleCellExperiment-class, assay runSCMerge.Rd: SingleCellExperiment-class, colData, assay, BiocParallelParam-class runScDblFinder.Rd: SingleCellExperiment-class, colData runScranSNN.Rd: SingleCellExperiment-class, reducedDim, assay, altExp, colData, igraph runScrublet.Rd: SingleCellExperiment-class, colData runSingleR.Rd: SingleCellExperiment-class runSoupX.Rd: SingleCellExperiment-class runTSCAN.Rd: SingleCellExperiment-class runTSCANClusterDEAnalysis.Rd: SingleCellExperiment-class runTSCANDEG.Rd: SingleCellExperiment-class runTSNE.Rd: SingleCellExperiment-class runUMAP.Rd: SingleCellExperiment-class, BiocParallelParam-class runVAM.Rd: SingleCellExperiment-class runZINBWaVE.Rd: SingleCellExperiment-class, colData, BiocParallelParam-class sampleSummaryStats.Rd: SingleCellExperiment-class, assay, colData scaterPCA.Rd: SingleCellExperiment-class, BiocParallelParam-class scaterlogNormCounts.Rd: logNormCounts sctkListGeneSetCollections.Rd: GeneSetCollection-class sctkPythonInstallConda.Rd: conda_install, reticulate, conda_create sctkPythonInstallVirtualEnv.Rd: virtualenv_install, reticulate, virtualenv_create selectSCTKConda.Rd: reticulate selectSCTKVirtualEnvironment.Rd: reticulate setRowNames.Rd: SingleCellExperiment-class setSCTKDisplayRow.Rd: SingleCellExperiment-class singleCellTK.Rd: SingleCellExperiment-class subsetSCECols.Rd: SingleCellExperiment-class subsetSCERows.Rd: SingleCellExperiment-class, altExp summarizeSCE.Rd: SingleCellExperiment-class 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed importGeneSetsFromMSigDB 51.256 0.535 52.048 plotDoubletFinderResults 42.141 0.247 42.559 runDoubletFinder 36.560 0.194 36.864 plotScDblFinderResults 31.970 0.829 32.959 runScDblFinder 21.457 0.475 22.040 importExampleData 14.622 1.854 16.979 plotBatchCorrCompare 14.218 0.140 14.426 plotScdsHybridResults 9.906 0.123 10.081 plotBcdsResults 9.388 0.148 9.572 plotDecontXResults 8.973 0.088 9.103 plotCxdsResults 7.767 0.064 7.859 runUMAP 7.707 0.070 7.809 runDecontX 7.628 0.070 7.729 plotUMAP 7.524 0.084 7.661 plotEmptyDropsResults 6.138 0.038 6.204 plotEmptyDropsScatter 6.048 0.031 6.103 runEmptyDrops 5.881 0.024 5.922 detectCellOutlier 5.690 0.165 5.893 convertSCEToSeurat 4.775 0.220 5.018 getEnrichRResult 0.311 0.041 6.382 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ 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/singleCellTK.Rcheck/00check.log’ for details.