############################################################################## ############################################################################## ### ### 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 4.4.0 (2024-04-24) * 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 12.7.4 * 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 50.094 1.493 60.304 plotDoubletFinderResults 47.369 0.345 51.439 runDoubletFinder 41.750 0.359 48.815 runScDblFinder 34.431 0.578 40.350 importExampleData 27.327 2.779 41.763 plotBatchCorrCompare 15.130 0.242 18.227 plotScdsHybridResults 13.901 0.218 16.622 plotTSCANClusterDEG 13.000 0.287 14.678 plotBcdsResults 12.632 0.386 14.450 plotDecontXResults 12.497 0.146 14.068 plotFindMarkerHeatmap 12.269 0.093 14.299 plotDEGViolin 11.059 0.201 12.228 plotEmptyDropsScatter 10.601 0.070 12.125 plotEmptyDropsResults 10.532 0.066 11.865 runEmptyDrops 9.936 0.079 11.666 plotCxdsResults 9.823 0.102 10.887 detectCellOutlier 9.697 0.228 11.675 convertSCEToSeurat 9.453 0.382 11.655 runSeuratSCTransform 9.606 0.138 11.749 runDecontX 9.443 0.086 11.081 plotDEGRegression 9.346 0.110 10.466 getFindMarkerTopTable 8.698 0.103 10.149 runUMAP 8.668 0.087 10.088 plotUMAP 8.561 0.100 10.014 runFindMarker 8.466 0.108 10.046 plotDEGHeatmap 7.456 0.165 8.640 plotTSCANPseudotimeHeatmap 5.873 0.080 6.887 plotTSCANDimReduceFeatures 5.738 0.092 7.133 plotTSCANPseudotimeGenes 5.585 0.090 6.898 plotTSCANClusterPseudo 5.410 0.103 7.396 plotTSCANResults 5.433 0.063 6.337 plotRunPerCellQCResults 5.402 0.049 6.220 importGeneSetsFromMSigDB 4.907 0.204 6.028 getTSCANResults 4.416 0.074 5.258 runFastMNN 4.211 0.080 5.333 plotMASTThresholdGenes 4.158 0.072 5.075 getEnrichRResult 0.740 0.059 5.242 * 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.