############################################################################## ############################################################################## ### ### 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 4.4.2 (2024-10-31) * 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 13.7.1 * 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 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 55.970 2.369 58.593 PlotDimRed 51.413 2.493 54.123 UpdateMetaclusters 16.624 1.064 17.695 PlotMarker 16.215 1.067 17.322 PlotOutliers 15.815 0.723 16.619 PlotStars 12.940 0.961 13.928 FlowSOM 12.694 1.039 13.859 GroupStats 12.336 0.799 13.168 PlotGroups 10.607 0.870 11.492 QueryMultiple 9.342 0.526 9.882 GetFlowJoLabels 8.871 0.749 9.626 query_multiple 8.984 0.579 9.585 AddAnnotation 8.884 0.518 9.423 Plot2DScatters 8.041 0.633 8.688 PlotManualBars 7.655 0.803 8.472 PlotNode 6.944 0.766 7.734 CountGroups 7.009 0.533 7.592 PlotVariable 6.758 0.708 7.507 PlotPies 6.654 0.695 7.365 PlotNumbers 6.575 0.740 7.346 QueryStarPlot 6.464 0.378 6.906 PlotFlowSOM 6.082 0.748 6.842 SaveClustersToFCS 5.785 0.865 6.655 PlotLabels 5.828 0.627 6.468 NMetaclusters 5.593 0.694 6.310 PlotOverview2D 5.444 0.607 6.060 TestOutliers 5.251 0.691 5.948 GetFeatures 5.538 0.387 5.989 MetaclusterCVs 5.368 0.505 5.880 print.FlowSOM 4.981 0.777 5.770 UpdateNodeSize 5.474 0.207 5.686 MetaclusterMFIs 4.897 0.702 5.635 NClusters 4.879 0.647 5.571 GetMetaclusterCVs 4.917 0.601 5.522 GetMetaclusterMFIs 4.830 0.674 5.517 GetMFIs 4.791 0.690 5.501 GetPercentages 4.835 0.553 5.409 GetMetaclusters 4.815 0.517 5.383 GetMetaclusterPercentagesPositive 4.736 0.579 5.317 GetCounts 4.639 0.591 5.286 FlowSOMSubset 4.791 0.366 5.215 GetClusters 4.637 0.492 5.160 GetClusterPercentagesPositive 4.660 0.458 5.157 GetClusterMFIs 4.407 0.659 5.073 * 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.