############################################################################## ############################################################################## ### ### 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_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.11.0’ * 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 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 ... 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 117.595 3.255 146.521 PlotDimRed 74.536 2.923 93.319 PlotMarker 50.838 1.319 59.588 UpdateMetaclusters 46.096 1.248 56.327 PlotStars 38.080 1.013 46.825 PlotOutliers 36.929 1.042 45.941 GroupStats 33.985 0.986 40.040 query_multiple 30.557 0.606 36.839 QueryMultiple 29.793 0.593 36.445 PlotGroups 28.456 1.010 33.896 FlowSOM 26.454 0.973 31.918 Plot2DScatters 22.601 0.799 28.097 AddAnnotation 22.194 0.759 27.173 QueryStarPlot 20.897 0.455 25.878 UpdateNodeSize 19.168 0.332 23.372 PlotNumbers 16.412 0.721 21.736 PlotNode 16.352 0.761 22.074 GetFlowJoLabels 15.932 0.732 20.652 PlotVariable 15.294 0.741 18.397 PlotManualBars 15.012 0.667 18.439 PlotPies 13.599 0.636 17.135 PlotFlowSOM 12.167 0.608 14.891 GetFeatures 12.018 0.439 14.916 CountGroups 11.378 0.577 14.459 PlotLabels 10.769 0.575 13.654 SaveClustersToFCS 9.588 0.714 12.225 NMetaclusters 8.986 0.728 11.675 TestOutliers 9.058 0.604 11.792 MetaclusterMFIs 9.047 0.598 12.043 NClusters 8.552 0.577 10.529 FlowSOMSubset 8.413 0.475 16.275 MetaclusterCVs 7.937 0.594 10.589 print.FlowSOM 7.960 0.567 10.081 GetMFIs 7.942 0.566 10.247 GetPercentages 7.891 0.594 10.258 PlotOverview2D 7.945 0.535 9.982 GetMetaclusters 7.862 0.591 9.916 GetClusters 7.881 0.547 10.646 GetMetaclusterPercentagesPositive 7.891 0.535 10.379 GetMetaclusterCVs 7.890 0.525 10.131 GetMetaclusterMFIs 7.860 0.543 10.432 GetClusterMFIs 7.610 0.516 10.052 GetCounts 7.599 0.424 9.560 GetClusterPercentagesPositive 7.535 0.462 9.796 NewData 7.306 0.441 9.165 ReadInput 6.584 0.487 8.420 MetaClustering 6.423 0.394 7.929 PlotSD 5.924 0.202 7.660 metaClustering_consensus 5.328 0.258 6.650 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.