############################################################################## ############################################################################## ### ### 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_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘2.12.0’ * 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 52.874 2.613 55.803 PlotDimRed 44.651 2.893 48.372 PlotOutliers 20.100 1.067 21.497 PlotMarker 19.475 1.298 21.038 UpdateMetaclusters 17.385 1.482 19.138 PlotStars 15.855 1.219 17.351 GroupStats 14.107 0.974 15.253 FlowSOM 12.578 1.152 13.933 PlotGroups 12.103 1.168 13.429 QueryMultiple 10.865 0.591 11.628 AddAnnotation 10.254 0.727 11.107 Plot2DScatters 9.940 0.844 10.959 query_multiple 9.992 0.607 10.764 GetFlowJoLabels 8.953 0.656 9.857 PlotManualBars 8.298 0.843 9.260 QueryStarPlot 8.057 0.422 8.590 PlotNode 7.536 0.906 8.575 PlotNumbers 7.233 0.933 8.314 PlotVariable 7.207 0.849 8.192 PlotPies 6.777 0.912 7.808 PlotFlowSOM 6.596 0.823 7.526 UpdateNodeSize 6.886 0.332 7.331 CountGroups 6.375 0.700 7.171 SaveClustersToFCS 5.800 0.910 6.865 NMetaclusters 5.560 0.847 6.527 PlotLabels 5.573 0.797 6.449 NClusters 5.421 0.925 6.449 PlotOverview2D 5.516 0.738 6.393 GetFeatures 5.768 0.436 6.274 MetaclusterMFIs 5.352 0.836 6.272 TestOutliers 5.272 0.884 6.354 print.FlowSOM 4.782 0.858 5.724 GetMetaclusterMFIs 4.852 0.715 5.659 GetPercentages 4.805 0.736 5.613 GetMetaclusterCVs 4.791 0.748 5.639 GetMFIs 4.788 0.746 5.609 MetaclusterCVs 4.752 0.748 5.588 GetMetaclusterPercentagesPositive 4.751 0.679 5.494 FlowSOMSubset 4.824 0.494 5.390 GetMetaclusters 4.560 0.702 5.340 NewData 4.594 0.642 5.315 GetClusterMFIs 4.625 0.476 5.161 * 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.