############################################################################## ############################################################################## ### ### 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_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.10.0’ * 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 ... OK * 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 63.913 2.899 67.407 PlotDimRed 42.362 2.926 45.952 PlotMarker 27.771 1.748 29.881 UpdateMetaclusters 24.129 2.004 26.684 PlotStars 20.097 1.452 21.803 PlotOutliers 20.389 1.138 21.765 GroupStats 17.450 1.251 18.906 PlotGroups 15.391 1.681 17.330 query_multiple 16.200 0.746 17.143 QueryMultiple 15.831 0.737 16.734 FlowSOM 14.604 1.262 16.079 Plot2DScatters 12.443 1.036 13.633 AddAnnotation 12.423 0.763 13.337 QueryStarPlot 10.919 0.519 11.573 PlotNumbers 9.031 1.016 10.191 PlotNode 8.638 1.106 9.865 PlotVariable 8.540 1.167 9.842 PlotPies 8.426 1.175 9.925 GetFlowJoLabels 8.669 0.790 9.568 UpdateNodeSize 9.071 0.332 9.520 PlotManualBars 8.238 1.048 9.399 PlotFlowSOM 7.415 1.035 8.569 CountGroups 6.468 0.788 7.454 PlotLabels 6.056 0.777 6.926 NMetaclusters 5.678 1.099 6.943 SaveClustersToFCS 5.376 1.228 6.723 NClusters 5.487 1.027 6.636 GetFeatures 5.908 0.501 6.492 MetaclusterMFIs 5.503 0.894 6.495 MetaclusterCVs 5.214 0.780 6.069 GetPercentages 4.936 0.885 5.934 print.FlowSOM 4.782 0.986 5.904 GetMetaclusterMFIs 4.913 0.854 5.857 PlotOverview2D 4.899 0.865 5.964 TestOutliers 4.959 0.794 5.835 GetMFIs 4.747 0.760 5.615 GetMetaclusters 4.676 0.827 5.615 GetMetaclusterPercentagesPositive 4.639 0.785 5.517 GetMetaclusterCVs 4.633 0.783 5.508 GetCounts 4.423 0.701 5.201 GetClusterPercentagesPositive 4.366 0.722 5.275 NewData 4.347 0.599 5.018 GetClusterMFIs 4.349 0.597 5.019 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.