############################################################################## ############################################################################## ### ### 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_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/FlowSOM.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.10.0’ * 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 15.0.0 (clang-1500.0.40.1)’ * 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 R 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 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 ... OK * 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 69.209 2.871 72.706 PlotDimRed 51.137 4.139 55.848 PlotMarker 23.912 1.206 25.180 UpdateMetaclusters 22.690 1.374 24.094 PlotStars 18.780 1.108 19.993 GroupStats 16.011 0.968 17.153 PlotOutliers 15.973 0.869 16.933 query_multiple 14.873 0.550 15.450 QueryMultiple 14.811 0.520 15.350 FlowSOM 14.393 0.807 15.263 PlotGroups 13.443 1.148 14.652 AddAnnotation 12.082 0.731 13.099 Plot2DScatters 10.422 0.645 11.318 QueryStarPlot 10.382 0.384 10.775 GetFlowJoLabels 9.261 0.807 10.154 PlotVariable 8.644 0.785 9.441 PlotNode 8.212 0.985 9.238 PlotNumbers 8.409 0.686 9.139 PlotPies 8.418 0.630 9.069 UpdateNodeSize 8.439 0.243 8.721 PlotManualBars 7.674 0.892 8.637 PlotFlowSOM 7.395 0.858 8.300 CountGroups 6.980 0.794 7.958 NMetaclusters 6.085 1.246 7.398 TestOutliers 5.938 0.751 6.762 SaveClustersToFCS 5.867 0.683 6.597 GetMetaclusterMFIs 5.436 1.033 6.525 PlotLabels 5.849 0.605 6.470 GetFeatures 5.719 0.681 6.527 MetaclusterMFIs 5.644 0.707 6.412 NClusters 5.548 0.726 6.332 MetaclusterCVs 5.508 0.729 6.292 GetMFIs 5.576 0.651 6.374 GetMetaclusterCVs 5.067 0.818 5.981 print.FlowSOM 5.015 0.703 5.730 GetMetaclusters 4.887 0.770 5.719 GetMetaclusterPercentagesPositive 4.895 0.731 5.762 GetPercentages 4.937 0.674 5.650 PlotOverview2D 4.880 0.601 5.514 GetClusterMFIs 4.772 0.629 5.545 GetClusterPercentagesPositive 4.663 0.704 5.371 GetCounts 4.621 0.651 5.325 GetClusters 4.569 0.654 5.228 NewData 4.270 0.685 5.016 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/FlowSOM.Rcheck/00check.log’ for details.