############################################################################## ############################################################################## ### ### 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_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.14.0’ * 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 91.018 2.340 97.118 PlotDimRed 73.576 2.730 78.205 PlotOutliers 38.030 1.129 40.522 PlotMarker 33.164 1.507 35.596 UpdateMetaclusters 32.069 1.342 34.971 PlotStars 27.795 1.172 30.559 GroupStats 26.024 1.131 27.946 PlotGroups 22.560 1.390 24.968 FlowSOM 22.419 1.354 24.474 AddAnnotation 17.097 0.807 18.390 query_multiple 17.273 0.616 18.505 QueryMultiple 17.025 0.546 18.330 Plot2DScatters 15.989 1.066 17.407 PlotManualBars 14.622 1.115 16.040 GetFlowJoLabels 13.451 0.570 14.405 PlotNode 12.945 0.977 14.492 PlotVariable 12.627 0.949 13.831 QueryStarPlot 12.795 0.420 13.613 PlotNumbers 12.119 0.873 13.249 PlotPies 12.045 0.885 14.907 UpdateNodeSize 12.216 0.362 12.760 GetFeatures 12.164 0.400 13.124 CountGroups 11.136 0.653 12.115 PlotFlowSOM 10.894 0.782 12.178 SaveClustersToFCS 9.767 0.857 11.440 PlotLabels 9.426 0.844 10.399 MetaclusterMFIs 9.072 1.183 10.439 NMetaclusters 9.337 0.865 11.531 NClusters 8.993 0.900 10.216 TestOutliers 8.906 0.730 10.402 GetPercentages 8.467 0.804 9.907 GetMFIs 7.843 1.170 9.118 FlowSOMSubset 8.377 0.448 9.104 GetMetaclusterMFIs 7.864 0.950 8.951 GetMetaclusterCVs 7.953 0.856 8.892 MetaclusterCVs 7.947 0.847 8.922 PlotOverview2D 8.180 0.612 9.702 print.FlowSOM 7.872 0.795 8.755 GetMetaclusterPercentagesPositive 7.840 0.822 8.776 GetMetaclusters 7.795 0.837 8.849 GetCounts 7.623 0.695 8.565 GetClusterMFIs 7.606 0.604 8.364 NewData 7.501 0.687 8.398 GetClusterPercentagesPositive 7.602 0.462 8.437 GetClusters 7.567 0.418 8.431 MetaClustering 6.582 0.787 7.512 ReadInput 6.749 0.519 7.842 metaClustering_consensus 5.270 0.489 5.964 * 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-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.