############################################################################## ############################################################################## ### ### 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 56.093 2.424 58.985 PlotDimRed 52.916 2.812 56.011 PlotMarker 16.419 1.018 17.514 UpdateMetaclusters 16.157 1.202 17.389 PlotOutliers 15.759 0.684 16.528 FlowSOM 12.738 0.917 13.691 GroupStats 12.483 0.852 13.364 PlotStars 12.335 0.792 13.150 PlotGroups 10.483 0.784 11.292 AddAnnotation 9.411 0.656 10.273 QueryMultiple 9.040 0.456 9.547 Plot2DScatters 8.133 0.610 8.759 query_multiple 8.046 0.355 8.448 GetFlowJoLabels 7.382 0.638 8.083 SaveClustersToFCS 6.635 0.885 7.541 PlotNumbers 6.544 0.609 7.183 PlotManualBars 6.510 0.550 7.095 PlotNode 6.383 0.608 7.036 CountGroups 6.250 0.716 6.990 PlotPies 6.416 0.530 6.979 PlotVariable 6.268 0.493 6.817 QueryStarPlot 6.093 0.264 6.405 NClusters 5.493 0.772 6.283 TestOutliers 5.439 0.685 6.134 PlotFlowSOM 5.414 0.579 6.041 UpdateNodeSize 5.683 0.286 5.976 GetFeatures 5.490 0.444 6.037 GetPercentages 5.305 0.584 5.906 print.FlowSOM 4.931 0.754 5.700 PlotLabels 5.112 0.470 5.614 GetMFIs 4.895 0.646 5.551 GetCounts 4.912 0.627 5.556 GetMetaclusterPercentagesPositive 4.863 0.648 5.521 MetaclusterMFIs 4.905 0.603 5.598 GetMetaclusters 4.865 0.628 5.512 GetMetaclusterMFIs 4.840 0.647 5.495 NMetaclusters 4.843 0.599 5.456 GetMetaclusterCVs 4.876 0.557 5.471 MetaclusterCVs 4.869 0.534 5.418 PlotOverview2D 4.794 0.595 5.420 FlowSOMSubset 4.840 0.524 5.413 GetClusterPercentagesPositive 4.537 0.605 5.158 GetClusters 4.482 0.586 5.079 GetClusterMFIs 4.488 0.563 5.059 * 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.