############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scran.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scran_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘scran/DESCRIPTION’ ... OK * this is package ‘scran’ version ‘1.36.0’ * 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 ‘scran’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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: buildSNNGraph.Rd: SingleCellExperiment-class, makeSNNGraph, makeKNNGraph, SummarizedExperiment-class, reducedDims, BiocSingularParam-class, BiocParallelParam-class, graph, cluster_walktrap clusterCells.Rd: SingleCellExperiment-class, clusterRows, SummarizedExperiment-class, BlusterParam-class combineBlocks.Rd: DataFrame-class, combineParallelPValues combineMarkers.Rd: DataFrame-class, BiocParallelParam-class, List-class, combineParallelPValues combinePValues.Rd: combineParallelPValues combineVar.Rd: DataFrame-class, combineParallelPValues computeSumFactors.Rd: pooledSizeFactors, computePooledFactors, sizeFactors convertTo.Rd: SingleCellExperiment-class correlateGenes.Rd: DataFrame-class correlateNull.Rd: BiocParallelParam-class correlatePairs.Rd: SummarizedExperiment-class, BiocParallelParam-class, DataFrame-class, parallelStouffer cyclone.Rd: SummarizedExperiment-class, BiocParallelParam-class decideTestsPerLabel.Rd: decideTests, List-class defunct.Rd: bootstrapStability, pairwiseModularity, neighborPurity, clusterRows, NNGraphParam-class, TwoStepParam-class, pairwiseRand denoisePCA.Rd: SummarizedExperiment-class, SingleCellExperiment-class, DataFrame-class, BiocSingularParam-class, BiocParallelParam-class, reducedDimNames, assays, reducedDims, LowRankMatrix-class, runSVD findMarkers.Rd: SummarizedExperiment-class, SingleCellExperiment-class, colLabels, DataFrame-class, BiocParallelParam-class fitTrendPoisson.Rd: BiocParallelParam-class fitTrendVar.Rd: weightedLowess fixedPCA.Rd: SingleCellExperiment-class, reducedDimNames, assays, BiocSingularParam-class, BiocParallelParam-class, reducedDims, LowRankMatrix-class gene_selection.Rd: Rle-class, SingleCellExperiment-class, calculateAverage getClusteredPCs.Rd: clusterRows, BlusterParam-class, makeSNNGraph, cluster_walktrap, DataFrame-class, List-class, runPCA getMarkerEffects.Rd: DataFrame-class getTopHVGs.Rd: DataFrame-class, SummarizedExperiment-class getTopMarkers.Rd: DataFrame-class, List-class modelGeneCV2.Rd: SummarizedExperiment-class, SingleCellExperiment-class, combineParallelPValues, BiocParallelParam-class, librarySizeFactors, sizeFactors, DataFrame-class modelGeneCV2WithSpikes.Rd: SummarizedExperiment-class, SingleCellExperiment-class, altExp, combineParallelPValues, BiocParallelParam-class, DataFrame-class, librarySizeFactors, sizeFactors modelGeneVar.Rd: SummarizedExperiment-class, combineParallelPValues, BiocParallelParam-class, DataFrame-class modelGeneVarByPoisson.Rd: SummarizedExperiment-class, SingleCellExperiment-class, combineParallelPValues, BiocParallelParam-class, librarySizeFactors, sizeFactors, DataFrame-class modelGeneVarWithSpikes.Rd: SummarizedExperiment-class, SingleCellExperiment-class, altExp, combineParallelPValues, BiocParallelParam-class, DataFrame-class, librarySizeFactors, sizeFactors multiMarkerStats.Rd: DataFrame-class, List-class pairwiseBinom.Rd: colLabels, BiocParallelParam-class, DataFrame-class, binomTest pairwiseTTests.Rd: SummarizedExperiment-class, SingleCellExperiment-class, colLabels, BiocParallelParam-class, DataFrame-class, logNormCounts pairwiseWilcox.Rd: SummarizedExperiment-class, SingleCellExperiment-class, colLabels, BiocParallelParam-class, DataFrame-class pseudoBulkDGE.Rd: DataFrame-class, makeContrasts, glmTreat, treat, voomWithQualityWeights, sumCountsAcrossCells, voom, List-class, topTags, topTable, metadata, filterByExpr pseudoBulkSpecific.Rd: treat, List-class, DataFrame-class quickCluster.Rd: SummarizedExperiment-class, NNGraphParam, HclustParam, BiocSingularParam-class, BiocParallelParam-class, dgCMatrix-class, calculateAverage quickSubCluster.Rd: SummarizedExperiment-class, SingleCellExperiment-class, BlusterParam-class, clusterRows, reducedDims, List-class, metadata sandbag.Rd: SummarizedExperiment-class scaledColRanks.Rd: BiocParallelParam-class scoreMarkers.Rd: SummarizedExperiment-class, BiocParallelParam-class, correctGroupSummary summaryMarkerStats.Rd: SummarizedExperiment-class, SingleCellExperiment-class, colLabels, DataFrame-class, sumCountsAcrossCells, BiocParallelParam-class, List-class testLinearModel.Rd: SummarizedExperiment-class, combineParallelPValues, BiocParallelParam-class, lmFit, fitLinearModel, DataFrame-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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning in combinePValues(p1, p2, p3) : 'combinePValues' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed cyclone 15.455 1.133 19.184 buildSNNGraph 10.329 0.272 12.176 pseudoBulkSpecific 8.762 0.115 9.937 decideTestsPerLabel 7.034 0.187 8.939 quickSubCluster 6.735 0.066 7.567 pseudoBulkDGE 6.066 0.088 6.741 findMarkers 4.391 0.056 5.209 * 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 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck/00check.log’ for details.