############################################################################## ############################################################################## ### ### 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_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.8.0’ * 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 R 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 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 ... NOTE PlotManualBars: no visible binding for global variable ‘MC’ PlotManualBars: no visible binding for global variable ‘Manual’ Undefined global functions or variables: MC Manual * checking Rd files ... OK * 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 93.362 2.326 124.937 PlotDimRed 74.261 2.595 101.373 PlotOutliers 34.918 0.750 45.317 UpdateMetaclusters 32.541 1.092 43.055 PlotMarker 32.219 0.999 43.130 PlotStars 27.892 0.817 36.760 GroupStats 26.006 0.906 36.077 PlotGroups 22.238 0.812 32.355 FlowSOM 22.081 0.893 30.750 QueryMultiple 17.164 0.416 21.952 AddAnnotation 16.916 0.659 23.360 query_multiple 17.027 0.428 21.676 PlotManualBars 15.661 0.684 21.944 Plot2DScatters 15.613 0.715 21.307 GetFlowJoLabels 13.656 0.843 24.739 PlotNode 12.815 0.636 17.867 QueryStarPlot 13.060 0.296 17.597 PlotVariable 12.165 0.622 15.723 PlotNumbers 11.967 0.572 16.377 PlotPies 11.788 0.590 15.690 GetFeatures 12.000 0.365 15.172 UpdateNodeSize 11.980 0.270 16.115 CountGroups 11.084 0.548 15.022 PlotFlowSOM 10.618 0.642 14.657 SaveClustersToFCS 9.678 0.812 14.276 NClusters 9.656 0.685 14.295 NMetaclusters 9.153 0.762 14.217 PlotLabels 9.303 0.481 13.174 MetaclusterMFIs 9.090 0.619 12.989 TestOutliers 8.847 0.649 11.851 GetMetaclusterPercentagesPositive 8.266 0.483 11.546 FlowSOMSubset 8.236 0.338 11.496 PlotOverview2D 8.015 0.538 10.804 MetaclusterCVs 7.940 0.549 11.123 GetMetaclusterCVs 7.944 0.521 11.521 GetMFIs 7.871 0.592 13.115 GetMetaclusterMFIs 7.905 0.470 11.055 GetPercentages 7.868 0.501 10.772 GetMetaclusters 7.869 0.478 10.952 print.FlowSOM 7.813 0.503 10.717 GetClusterMFIs 7.605 0.480 11.277 GetClusterPercentagesPositive 7.520 0.423 10.612 GetCounts 7.533 0.398 10.190 GetClusters 7.482 0.439 10.674 NewData 7.373 0.429 10.987 ReadInput 6.640 0.516 9.559 MetaClustering 6.450 0.527 9.779 metaClustering_consensus 5.653 0.366 8.071 PlotSD 4.111 0.105 5.539 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.