############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings singleCellTK_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/singleCellTK.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘2.15.0’ * 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 47.523 0.339 47.954 plotDoubletFinderResults 42.381 0.218 42.690 plotScDblFinderResults 40.323 0.570 41.006 runDoubletFinder 38.355 0.147 38.577 runScDblFinder 30.330 0.240 30.631 importExampleData 24.723 1.137 31.475 plotBatchCorrCompare 13.814 0.117 13.939 plotScdsHybridResults 12.196 0.204 11.326 plotBcdsResults 10.849 0.068 9.835 plotDecontXResults 9.771 0.116 9.905 runDecontX 8.625 0.084 8.726 runUMAP 8.007 0.064 8.078 plotCxdsResults 8.034 0.024 8.066 plotUMAP 7.922 0.060 7.994 plotTSCANClusterDEG 7.204 0.031 7.251 detectCellOutlier 6.805 0.080 6.901 plotDEGViolin 6.322 0.227 6.562 plotFindMarkerHeatmap 6.437 0.051 6.503 plotEmptyDropsScatter 5.922 0.072 6.005 plotEmptyDropsResults 5.938 0.016 5.963 convertSCEToSeurat 5.603 0.080 5.694 runEmptyDrops 5.545 0.012 5.562 plotDEGRegression 5.098 0.020 5.128 getEnrichRResult 0.389 0.012 8.624 runEnrichR 0.387 0.005 7.994 * 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-3.20-bioc/meat/singleCellTK.Rcheck/00check.log’ for details.