############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.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 ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.12.0’ * 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 ‘FlowSOM’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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) PlotDimRed.Rd:55: Lost braces 55 | of the dimred default = function(dimred){dimred$Y}.} | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed FlowSOMmary 99.286 2.815 121.629 PlotDimRed 78.043 2.604 95.501 PlotOutliers 40.662 1.036 47.076 PlotMarker 36.320 1.119 44.159 UpdateMetaclusters 34.859 1.084 39.842 PlotStars 30.270 0.980 35.838 GroupStats 28.364 0.998 34.943 PlotGroups 23.924 1.012 29.845 FlowSOM 23.560 1.318 30.874 QueryMultiple 19.766 0.523 23.362 query_multiple 19.667 0.561 22.811 AddAnnotation 18.225 0.656 21.724 Plot2DScatters 16.616 0.723 20.635 PlotManualBars 15.470 0.768 18.901 GetFlowJoLabels 14.539 0.846 21.714 PlotNode 14.089 0.682 18.257 QueryStarPlot 14.165 0.387 16.510 UpdateNodeSize 13.655 0.293 15.289 PlotNumbers 13.042 0.666 16.428 PlotPies 12.771 0.754 15.183 PlotVariable 12.801 0.638 15.312 GetFeatures 12.754 0.544 16.439 CountGroups 11.822 0.590 14.076 PlotFlowSOM 11.235 0.684 14.648 SaveClustersToFCS 10.521 0.783 12.949 PlotLabels 10.015 0.600 12.493 NClusters 9.598 0.699 12.184 MetaclusterMFIs 9.579 0.647 12.010 NMetaclusters 9.464 0.665 12.114 TestOutliers 9.302 0.613 11.334 MetaclusterCVs 8.789 0.672 11.498 FlowSOMSubset 8.880 0.519 14.830 GetMetaclusters 8.546 0.705 12.896 GetPercentages 8.323 0.716 13.726 PlotOverview2D 8.513 0.514 10.085 GetMFIs 8.321 0.592 10.723 GetMetaclusterPercentagesPositive 8.188 0.718 13.793 print.FlowSOM 8.243 0.654 9.793 GetMetaclusterCVs 8.301 0.577 10.244 GetMetaclusterMFIs 8.269 0.575 10.431 GetCounts 7.904 0.566 12.152 GetClusterPercentagesPositive 7.921 0.499 9.855 NewData 7.888 0.501 9.956 GetClusterMFIs 7.866 0.504 9.915 GetClusters 7.821 0.453 9.639 ReadInput 6.881 0.515 8.308 MetaClustering 6.738 0.493 8.499 metaClustering_consensus 5.345 0.399 6.713 PlotSD 4.524 0.163 5.394 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.