############################################################################## ############################################################################## ### ### 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_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘singleCellTK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘singleCellTK’ version ‘2.14.0’ * 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 ‘singleCellTK’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: R 1.0Mb extdata 1.5Mb shiny 2.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... NOTE checkRd: (-1) dedupRowNames.Rd:10: Lost braces 10 | \item{x}{A matrix like or /linkS4class{SingleCellExperiment} object, on which | ^ checkRd: (-1) dedupRowNames.Rd:14: Lost braces 14 | /linkS4class{SingleCellExperiment} object. When set to \code{TRUE}, will | ^ checkRd: (-1) dedupRowNames.Rd:22: Lost braces 22 | By default, a matrix or /linkS4class{SingleCellExperiment} object | ^ checkRd: (-1) dedupRowNames.Rd:24: Lost braces 24 | When \code{x} is a /linkS4class{SingleCellExperiment} and \code{as.rowData} | ^ checkRd: (-1) plotBubble.Rd:42: Lost braces 42 | \item{scale}{Option to scale the data. Default: /code{FALSE}. Selected assay will not be scaled.} | ^ checkRd: (-1) runClusterSummaryMetrics.Rd:27: Lost braces 27 | \item{scale}{Option to scale the data. Default: /code{FALSE}. Selected assay will not be scaled.} | ^ checkRd: (-1) runEmptyDrops.Rd:66: Lost braces 66 | provided \\linkS4class{SingleCellExperiment} object. | ^ checkRd: (-1) runSCMerge.Rd:44: Lost braces 44 | construct pseudo-replicates. The length of code{kmeansK} needs to be the same | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 plotScDblFinderResults 49.893 1.211 63.693 plotDoubletFinderResults 47.987 0.396 56.453 runDoubletFinder 41.258 0.292 49.935 runScDblFinder 33.057 0.560 39.496 importExampleData 27.888 2.867 37.714 plotBatchCorrCompare 15.109 0.237 18.558 plotScdsHybridResults 13.855 0.200 17.772 plotTSCANClusterDEG 13.275 0.219 17.035 plotBcdsResults 12.702 0.393 16.374 plotDecontXResults 12.347 0.195 14.944 plotFindMarkerHeatmap 12.272 0.106 14.851 plotDEGViolin 11.046 0.237 13.463 plotEmptyDropsScatter 10.637 0.073 12.917 plotEmptyDropsResults 10.593 0.090 13.198 detectCellOutlier 9.847 0.210 11.848 runSeuratSCTransform 9.870 0.149 11.889 runEmptyDrops 9.926 0.058 11.940 runDecontX 9.820 0.081 11.997 convertSCEToSeurat 9.352 0.356 11.405 plotCxdsResults 9.543 0.119 11.560 plotDEGRegression 9.257 0.125 11.104 plotUMAP 8.670 0.086 10.500 getFindMarkerTopTable 8.625 0.104 10.210 runUMAP 8.626 0.073 9.897 runFindMarker 8.532 0.088 10.120 plotDEGHeatmap 7.443 0.189 9.170 plotTSCANPseudotimeHeatmap 5.848 0.057 7.211 plotTSCANDimReduceFeatures 5.825 0.053 7.295 plotTSCANClusterPseudo 5.715 0.058 7.073 plotTSCANPseudotimeGenes 5.578 0.054 7.042 plotRunPerCellQCResults 5.397 0.048 6.411 plotTSCANResults 5.368 0.053 6.511 importGeneSetsFromMSigDB 4.951 0.190 6.208 getTSCANResults 4.434 0.073 5.274 runFastMNN 4.287 0.071 5.161 plotMASTThresholdGenes 4.185 0.066 5.057 getEnrichRResult 0.739 0.056 11.605 runEnrichR 0.690 0.044 7.894 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck/00check.log’ for details.