############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings scater_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/scater.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * 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 ‘scater/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scater’ version ‘1.35.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 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 ‘scater’ 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 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: accessors.Rd: SingleCellExperiment annotateBMFeatures.Rd: SingleCellExperiment, SingleCellExperiment-class, DataFrame-class, rowData bootstraps.Rd: SingleCellExperiment getExplanatoryPCs.Rd: SingleCellExperiment-class getVarianceExplained.Rd: SummarizedExperiment-class, DataFrame-class, BiocParallelParam-class ggsce.Rd: ggplot, SingleCellExperiment-class, aes nexprs.Rd: SummarizedExperiment-class, BiocParallelParam-class, DelayedMatrix-class plotColData.Rd: SingleCellExperiment-class, geom_hex, ggplot plotDots.Rd: SingleCellExperiment-class, colData, correctGroupSummary, ggplot plotExpression.Rd: geom_hex plotGroupedHeatmap.Rd: SingleCellExperiment-class, colData, correctGroupSummary plotHeatmap.Rd: SingleCellExperiment-class plotHighestExprs.Rd: ggplot plotRLE.Rd: BiocParallelParam-class, DelayedArray plotReducedDim.Rd: geom_hex plotRowData.Rd: ggplot plotScater.Rd: SingleCellExperiment-class, facet_wrap, ggplot plot_reddim.Rd: reducedDims, ggplot projectReducedDim.Rd: SummarizedExperiment-class, SingleCellExperiment-class retrieveCellInfo.Rd: SingleCellExperiment-class, DataFrame-class, colData, assay, altExps retrieveFeatureInfo.Rd: SingleCellExperiment-class, DataFrame-class, rowData, assay runColDataPCA.Rd: SingleCellExperiment-class, BiocSingularParam-class, BiocParallelParam-class runMDS.Rd: SummarizedExperiment-class, SingleCellExperiment-class, reducedDims, reducedDim, altExp runMultiUMAP.Rd: SummarizedExperiment-class, SingleCellExperiment-class, reducedDims, altExps runNMF.Rd: SummarizedExperiment-class, SingleCellExperiment-class, reducedDims, reducedDim, altExp runPCA.Rd: SummarizedExperiment-class, SingleCellExperiment-class, BiocSingularParam-class, BiocParallelParam-class, reducedDims, bsparam, reducedDim, altExp runTSNE.Rd: SummarizedExperiment-class, SingleCellExperiment-class, MulticoreParam-class, findKNN, BiocNeighborParam-class, BiocParallelParam-class, reducedDims, reducedDim, altExp runUMAP.Rd: SummarizedExperiment-class, SingleCellExperiment-class, MulticoreParam-class, findKNN, BiocNeighborParam-class, BiocParallelParam-class, reducedDims, reducedDim, altExp scater-plot-args.Rd: ggplot, DataFrame-class toSingleCellExperiment.Rd: SingleCellExperiment 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 plotRLE 6.542 0.113 6.655 plotReducedDim 5.476 0.221 5.191 runMultiUMAP 5.320 0.003 5.324 * 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 NOTE See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/scater.Rcheck/00check.log’ for details.