############################################################################## ############################################################################## ### ### 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 56.861 2.482 59.742 PlotDimRed 52.949 3.167 56.354 PlotMarker 16.519 1.247 17.799 UpdateMetaclusters 16.179 1.133 17.332 PlotOutliers 15.829 0.620 16.506 PlotStars 13.932 0.906 14.871 FlowSOM 12.795 1.083 14.075 GroupStats 12.185 0.920 13.124 PlotGroups 10.917 1.009 11.950 query_multiple 9.158 0.655 9.832 QueryMultiple 8.914 0.588 9.526 AddAnnotation 8.809 0.565 9.381 GetFlowJoLabels 7.961 0.839 8.817 Plot2DScatters 8.042 0.715 8.767 CountGroups 7.339 0.630 8.035 PlotManualBars 7.049 0.705 7.789 PlotNode 6.651 0.706 7.366 PlotNumbers 6.531 0.712 7.258 PlotVariable 6.302 0.710 7.041 SaveClustersToFCS 6.234 0.734 6.980 QueryStarPlot 6.410 0.480 6.956 PlotPies 6.151 0.710 6.910 PlotLabels 5.505 0.637 6.159 PlotFlowSOM 5.486 0.631 6.138 GetMetaclusterCVs 5.346 0.701 6.072 NMetaclusters 5.370 0.628 6.004 UpdateNodeSize 5.695 0.277 5.983 MetaclusterCVs 5.326 0.601 5.981 TestOutliers 5.253 0.673 5.955 GetFeatures 5.448 0.454 5.907 MetaclusterMFIs 5.124 0.572 5.741 GetMFIs 4.852 0.774 5.640 print.FlowSOM 4.904 0.694 5.635 PlotOverview2D 4.996 0.583 5.593 GetMetaclusters 4.854 0.704 5.571 NClusters 4.908 0.608 5.599 GetPercentages 4.879 0.568 5.463 GetMetaclusterMFIs 4.723 0.626 5.353 GetCounts 4.710 0.620 5.453 GetClusterMFIs 4.702 0.554 5.319 GetClusters 4.574 0.546 5.148 GetMetaclusterPercentagesPositive 4.403 0.707 5.145 GetClusterPercentagesPositive 4.668 0.420 5.140 * 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.