############################################################################## ############################################################################## ### ### 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 90.627 2.443 97.751 PlotDimRed 73.911 2.912 79.472 PlotOutliers 38.874 1.018 45.875 PlotMarker 33.599 1.599 37.156 UpdateMetaclusters 31.869 1.370 34.535 PlotStars 27.349 1.083 29.124 GroupStats 26.086 1.076 27.635 FlowSOM 22.263 1.271 24.435 PlotGroups 22.015 1.328 23.759 AddAnnotation 16.963 0.820 18.436 QueryMultiple 17.206 0.505 18.539 query_multiple 16.971 0.584 18.126 Plot2DScatters 15.651 0.765 16.862 PlotManualBars 14.746 1.124 16.121 GetFlowJoLabels 13.541 0.714 14.497 PlotNode 12.871 0.824 14.040 QueryStarPlot 12.710 0.380 13.728 PlotVariable 11.907 1.095 13.294 PlotNumbers 12.015 0.930 13.231 PlotPies 12.030 0.841 14.092 UpdateNodeSize 12.262 0.258 13.350 GetFeatures 11.958 0.560 12.936 CountGroups 11.381 0.776 12.389 PlotFlowSOM 10.325 0.707 11.597 SaveClustersToFCS 10.026 0.864 11.412 PlotLabels 9.422 0.649 10.260 NMetaclusters 9.035 0.989 10.635 MetaclusterMFIs 8.956 0.992 10.464 NClusters 9.097 0.809 10.416 TestOutliers 8.826 0.612 9.717 MetaclusterCVs 8.050 1.086 9.249 PlotOverview2D 8.091 0.696 9.202 FlowSOMSubset 8.346 0.405 9.128 GetMetaclusterMFIs 7.911 0.792 8.920 print.FlowSOM 7.877 0.775 9.126 GetMetaclusters 7.816 0.800 8.923 GetMFIs 7.803 0.806 8.783 GetMetaclusterCVs 7.900 0.697 8.742 GetPercentages 7.908 0.650 9.081 GetMetaclusterPercentagesPositive 7.851 0.589 8.660 GetCounts 7.827 0.551 8.712 GetClusterPercentagesPositive 7.619 0.579 8.546 GetClusters 7.521 0.584 8.312 NewData 7.495 0.587 8.260 GetClusterMFIs 7.515 0.542 8.292 MetaClustering 6.411 0.889 7.407 ReadInput 6.745 0.534 7.952 metaClustering_consensus 5.599 0.645 6.581 * 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.