############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scran_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘scran/DESCRIPTION’ ... OK * this is package ‘scran’ version ‘1.35.0’ * 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... INFO installed size is 5.2Mb sub-directories of 1Mb or more: libs 4.2Mb * 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 loading without being on the library search path ... 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 12.055 0.044 12.100 buildSNNGraph 6.072 0.055 6.126 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck/00check.log’ for details.