############################################################################## ############################################################################## ### ### 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/meat/FlowSOM.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-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 Monterey 12.7.1 * 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 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 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 114.512 2.734 124.697 PlotDimRed 74.506 2.535 81.618 PlotMarker 48.978 1.179 53.684 UpdateMetaclusters 44.136 1.318 46.887 PlotStars 36.774 1.088 40.564 PlotOutliers 35.741 0.816 38.173 GroupStats 32.505 1.022 35.439 QueryMultiple 29.141 0.520 32.024 PlotGroups 27.352 1.029 30.448 query_multiple 27.399 0.719 31.921 FlowSOM 25.463 1.427 27.900 Plot2DScatters 21.604 0.669 23.306 AddAnnotation 21.233 0.756 22.558 QueryStarPlot 20.280 0.383 21.489 UpdateNodeSize 17.647 0.256 18.244 PlotNumbers 16.087 0.799 18.751 PlotNode 16.135 0.696 19.530 GetFlowJoLabels 15.474 0.682 17.198 PlotVariable 14.909 0.607 16.281 PlotManualBars 14.686 0.748 16.672 PlotPies 13.926 0.735 16.248 PlotFlowSOM 12.322 0.748 13.645 GetFeatures 12.067 0.428 13.069 CountGroups 11.351 0.806 12.362 PlotLabels 10.541 0.575 12.310 SaveClustersToFCS 9.371 0.876 10.363 NMetaclusters 8.972 0.809 10.573 MetaclusterMFIs 9.089 0.601 10.539 NClusters 8.988 0.636 10.212 TestOutliers 8.524 0.581 9.211 MetaclusterCVs 8.242 0.621 9.662 GetMetaclusterMFIs 8.120 0.563 9.588 FlowSOMSubset 7.967 0.549 8.691 PlotOverview2D 7.961 0.502 8.937 print.FlowSOM 7.597 0.820 10.367 GetPercentages 7.812 0.587 9.351 GetMetaclusters 7.692 0.702 8.792 GetMetaclusterPercentagesPositive 7.775 0.586 8.881 GetMFIs 7.780 0.569 8.829 GetMetaclusterCVs 7.797 0.548 8.770 GetCounts 7.547 0.514 8.432 GetClusterMFIs 7.442 0.469 8.626 GetClusterPercentagesPositive 7.421 0.477 8.345 GetClusters 7.366 0.454 8.348 NewData 7.244 0.466 8.035 ReadInput 6.521 0.675 7.474 MetaClustering 5.786 0.463 6.545 PlotSD 5.448 0.157 6.069 metaClustering_consensus 5.069 0.348 5.808 * 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/meat/FlowSOM.Rcheck/00check.log’ for details.