############################################################################## ############################################################################## ### ### 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 4.4.0 (2024-04-24) * 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 61.207 2.751 64.579 PlotDimRed 52.946 3.519 57.039 UpdateMetaclusters 18.146 1.185 19.433 PlotMarker 18.021 0.998 19.131 PlotOutliers 17.199 0.591 17.919 PlotStars 14.827 0.965 15.909 GroupStats 13.336 0.985 14.720 FlowSOM 12.541 1.057 14.049 PlotGroups 11.678 0.863 12.612 AddAnnotation 10.664 0.662 14.069 QueryMultiple 10.130 0.476 10.705 query_multiple 10.112 0.475 10.646 GetFlowJoLabels 8.658 0.626 9.496 Plot2DScatters 8.605 0.627 9.506 PlotManualBars 8.493 0.636 9.177 PlotNumbers 7.739 0.723 8.507 PlotVariable 7.364 0.796 8.234 CountGroups 7.206 0.772 9.397 QueryStarPlot 7.527 0.425 8.039 PlotNode 7.185 0.654 7.885 PlotPies 7.075 0.751 7.910 MetaclusterMFIs 6.895 0.805 7.759 PlotFlowSOM 6.557 0.656 7.253 NClusters 6.362 0.732 7.173 SaveClustersToFCS 6.234 0.730 6.992 UpdateNodeSize 6.371 0.256 6.655 NMetaclusters 5.769 0.826 6.734 PlotLabels 5.924 0.502 6.480 GetFeatures 6.005 0.381 6.515 MetaclusterCVs 5.807 0.576 6.432 GetMetaclusterPercentagesPositive 5.704 0.678 6.414 TestOutliers 5.669 0.626 6.317 GetMFIs 5.413 0.667 6.421 print.FlowSOM 5.349 0.690 6.069 GetMetaclusters 5.274 0.743 6.052 PlotOverview2D 5.487 0.502 6.041 GetMetaclusterMFIs 5.260 0.560 5.851 GetMetaclusterCVs 5.219 0.571 5.869 GetCounts 5.304 0.427 5.784 FlowSOMSubset 5.288 0.434 5.755 GetPercentages 5.124 0.595 5.932 GetClusterPercentagesPositive 4.873 0.561 5.490 GetClusterMFIs 4.797 0.570 5.405 GetClusters 4.807 0.508 5.360 NewData 4.677 0.393 5.221 * 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.