############################################################################## ############################################################################## ### ### 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 47.607 1.207 59.148 plotDoubletFinderResults 48.024 0.408 54.312 runDoubletFinder 41.212 0.271 46.628 runScDblFinder 33.671 0.561 37.979 importExampleData 27.586 2.963 43.146 plotBatchCorrCompare 15.317 0.213 17.989 plotScdsHybridResults 14.153 0.192 17.122 plotTSCANClusterDEG 13.368 0.195 15.976 plotBcdsResults 12.578 0.396 15.622 plotDecontXResults 12.308 0.148 14.144 plotFindMarkerHeatmap 12.049 0.104 14.554 plotDEGViolin 11.358 0.215 13.040 plotEmptyDropsScatter 10.567 0.073 12.434 plotEmptyDropsResults 10.541 0.074 12.246 detectCellOutlier 9.888 0.221 12.154 runEmptyDrops 9.874 0.060 11.262 runDecontX 9.735 0.074 11.101 runSeuratSCTransform 9.628 0.166 11.802 convertSCEToSeurat 9.358 0.386 12.365 plotCxdsResults 9.625 0.110 10.820 plotDEGRegression 9.581 0.128 11.250 getFindMarkerTopTable 8.663 0.127 10.367 plotUMAP 8.691 0.083 9.839 runFindMarker 8.427 0.086 9.579 runUMAP 8.250 0.096 9.602 plotDEGHeatmap 7.357 0.166 9.652 plotTSCANPseudotimeHeatmap 5.814 0.051 6.577 plotTSCANClusterPseudo 5.720 0.055 6.573 plotTSCANDimReduceFeatures 5.692 0.052 6.606 plotRunPerCellQCResults 5.494 0.052 6.602 plotTSCANPseudotimeGenes 5.452 0.047 6.399 plotTSCANResults 5.365 0.051 6.044 importGeneSetsFromMSigDB 4.941 0.179 5.967 getTSCANResults 4.410 0.079 5.269 plotMASTThresholdGenes 4.096 0.061 5.133 * 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.