############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings singleCellTK_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 6.9Mb sub-directories of 1Mb or more: extdata 1.6Mb shiny 3.0Mb * 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 loading without being on the library search path ... 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 runSeuratSCTransform 47.109 0.383 47.607 plotDoubletFinderResults 42.120 0.136 42.326 plotScDblFinderResults 41.098 0.367 41.541 runDoubletFinder 37.924 0.155 38.152 runScDblFinder 29.872 0.255 30.179 importExampleData 22.477 1.661 29.937 plotBatchCorrCompare 13.458 0.200 13.665 plotScdsHybridResults 12.285 0.181 11.349 plotBcdsResults 10.559 0.202 9.668 plotDecontXResults 9.527 0.120 9.666 runDecontX 8.305 0.092 8.413 runUMAP 8.333 0.044 8.387 detectCellOutlier 7.894 0.219 8.131 plotCxdsResults 7.909 0.019 7.938 plotUMAP 7.787 0.032 7.827 plotTSCANClusterDEG 7.540 0.043 7.601 plotFindMarkerHeatmap 6.380 0.023 6.419 plotDEGViolin 6.179 0.064 6.256 convertSCEToSeurat 5.672 0.422 6.106 plotEmptyDropsResults 5.891 0.004 5.903 plotEmptyDropsScatter 5.849 0.024 5.878 getFindMarkerTopTable 5.259 0.427 5.699 runEmptyDrops 5.539 0.004 5.546 runFindMarker 5.059 0.291 5.364 plotDEGRegression 5.213 0.012 5.236 getEnrichRResult 0.423 0.096 8.590 runEnrichR 0.418 0.043 8.362 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck/00check.log’ for details.