############################################################################## ############################################################################## ### ### 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_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.2.0’ * 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 * 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 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 89.016 2.469 91.703 PlotDimRed 69.913 1.267 71.258 UpdateMetaclusters 34.732 1.699 36.479 PlotMarker 30.783 1.669 32.494 GroupStats 25.869 1.596 27.500 PlotGroups 22.296 2.296 24.659 FlowSOM 22.015 1.612 23.660 AddAnnotation 16.447 1.012 17.483 UpdateNodeSize 15.154 0.365 15.536 query_multiple 14.955 0.384 15.361 QueryMultiple 14.286 0.475 14.928 PlotNode 12.435 1.130 13.623 PlotStars 12.103 0.978 13.150 Plot2DScatters 10.869 0.896 11.796 PlotFlowSOM 10.410 1.313 11.737 QueryStarPlot 11.276 0.401 11.734 GetFlowJoLabels 10.597 0.741 11.355 PlotManualBars 10.227 0.944 11.190 PlotNumbers 9.750 1.167 10.932 PlotPies 10.040 0.783 10.835 CountGroups 8.084 0.898 8.993 PlotLabels 7.291 0.959 8.264 TestOutliers 7.073 0.975 8.064 SaveClustersToFCS 6.968 1.020 8.089 NMetaclusters 6.665 1.057 7.742 PlotVariable 6.995 0.636 7.640 MetaclusterMFIs 6.681 0.920 7.617 NClusters 6.512 0.762 7.289 GetFeatures 6.770 0.332 7.111 GetMetaclusterCVs 6.050 0.849 6.922 GetMetaclusters 5.814 1.014 6.839 FlowSOMSubset 6.384 0.427 6.827 GetPercentages 5.791 1.020 6.822 MetaclusterCVs 5.798 0.999 6.811 GetClusterMFIs 6.207 0.491 6.732 GetMetaclusterMFIs 5.839 0.810 6.660 print.FlowSOM 5.838 0.780 6.626 ReadInput 5.749 0.847 6.601 GetMFIs 5.741 0.854 6.621 PlotOverview2D 5.809 0.743 6.558 GetCounts 5.919 0.516 6.482 GetClusters 5.803 0.469 6.282 NewData 5.235 0.489 5.737 MetaClustering 4.634 0.682 5.329 * 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-3.14-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.