############################################################################## ############################################################################## ### ### 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_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ 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 ‘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 90.244 2.514 96.635 PlotDimRed 73.778 2.802 79.011 PlotOutliers 38.020 0.967 40.427 PlotMarker 32.535 1.373 34.637 UpdateMetaclusters 32.285 1.294 36.220 PlotStars 27.320 1.142 29.571 GroupStats 25.058 0.991 26.299 PlotGroups 22.161 1.255 24.263 FlowSOM 22.190 0.979 24.441 QueryMultiple 17.162 0.578 19.766 AddAnnotation 16.880 0.794 18.396 query_multiple 17.009 0.511 18.360 Plot2DScatters 15.579 0.999 16.798 PlotManualBars 14.936 0.822 16.703 PlotNode 13.298 0.874 14.394 GetFlowJoLabels 13.523 0.615 14.716 QueryStarPlot 12.763 0.454 14.072 PlotVariable 12.334 0.783 15.190 PlotNumbers 12.039 0.860 13.277 GetFeatures 12.211 0.460 12.963 UpdateNodeSize 12.192 0.267 13.421 PlotPies 11.416 0.847 12.775 CountGroups 11.464 0.583 12.964 PlotFlowSOM 10.260 0.872 11.358 MetaclusterMFIs 10.008 0.867 11.300 SaveClustersToFCS 9.660 0.848 10.797 PlotLabels 9.382 0.688 10.334 NClusters 9.162 0.883 10.499 TestOutliers 8.811 0.781 10.074 NMetaclusters 8.642 0.821 10.075 FlowSOMSubset 8.592 0.554 9.344 PlotOverview2D 8.135 0.787 9.489 GetMetaclusters 8.086 0.773 9.002 GetMFIs 8.014 0.667 9.253 GetMetaclusterCVs 7.907 0.739 8.818 MetaclusterCVs 7.954 0.654 9.054 GetMetaclusterPercentagesPositive 7.775 0.777 8.660 GetPercentages 7.731 0.782 8.619 print.FlowSOM 7.715 0.792 8.603 GetMetaclusterMFIs 7.899 0.602 8.929 GetClusterPercentagesPositive 7.529 0.675 8.355 GetCounts 7.542 0.526 8.250 NewData 7.367 0.658 8.543 GetClusters 7.436 0.574 8.132 GetClusterMFIs 7.488 0.459 8.477 ReadInput 6.627 0.522 8.071 MetaClustering 6.525 0.602 7.323 metaClustering_consensus 5.330 0.443 6.087 * 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-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.