############################################################################## ############################################################################## ### ### 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 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.6 * 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 15.0.0 (clang-1500.0.40.1)’ * 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 60.313 2.803 63.801 PlotDimRed 53.038 3.333 56.877 PlotMarker 18.855 1.104 20.068 UpdateMetaclusters 17.953 1.138 19.194 PlotOutliers 17.991 0.728 18.825 PlotStars 15.744 0.971 16.810 GroupStats 13.501 0.887 14.647 FlowSOM 13.056 1.079 14.300 PlotGroups 11.788 0.988 12.867 AddAnnotation 10.529 0.665 13.502 query_multiple 10.175 0.489 10.699 QueryMultiple 9.857 0.393 10.320 Plot2DScatters 8.719 0.725 9.611 GetFlowJoLabels 8.703 0.613 9.496 PlotManualBars 8.248 0.708 9.007 PlotVariable 7.376 0.719 8.149 PlotNode 7.300 0.659 8.002 QueryStarPlot 7.388 0.408 7.891 PlotFlowSOM 7.046 0.711 7.798 PlotNumbers 7.011 0.736 7.797 CountGroups 6.895 0.665 8.536 PlotPies 6.662 0.550 7.344 SaveClustersToFCS 6.246 0.767 7.040 PlotLabels 6.290 0.608 6.935 NClusters 6.088 0.809 7.058 NMetaclusters 6.025 0.733 6.939 MetaclusterMFIs 5.814 0.760 6.625 GetPercentages 5.826 0.663 6.693 UpdateNodeSize 6.197 0.220 6.450 GetFeatures 5.985 0.416 6.497 TestOutliers 5.684 0.673 6.386 GetMetaclusterMFIs 5.648 0.677 6.409 PlotOverview2D 5.537 0.526 6.110 GetMetaclusters 5.365 0.692 6.211 MetaclusterCVs 5.242 0.727 6.006 print.FlowSOM 5.291 0.655 5.974 GetMetaclusterPercentagesPositive 5.246 0.618 5.949 GetMFIs 5.274 0.547 5.849 GetMetaclusterCVs 4.896 0.589 5.585 GetCounts 4.974 0.510 5.591 GetClusters 4.939 0.500 5.518 GetClusterPercentagesPositive 4.856 0.512 5.417 GetClusterMFIs 4.777 0.482 5.288 NewData 4.511 0.487 5.063 * 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.